A B C D E F G H I J L M N O P Q R S T U V W X Z

A

AbortLoadIndexPageController - Class in net.sourceforge.solexatools.webapp.controller

AbortLoadIndexPageController class.

AbortLoadIndexPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AbortLoadIndexPageController

Constructor for AbortLoadIndexPageController.

AbstractFacade<T> - Class in io.seqware.webservice.generated.controller

AbstractFacade(Class<T>) - Constructor for class io.seqware.webservice.generated.controller.AbstractFacade

AbstractJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model

AbstractJob(String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

for bash Job

AbstractJob(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

for Java/Perl/JavaModule job

AbstractWorkflowDataModel - Class in net.sourceforge.seqware.pipeline.workflowV2

AbstractWorkflowDataModel() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

AbstractWorkflowEngine - Class in net.sourceforge.seqware.pipeline.workflowV2

AbstractWorkflowEngine() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine

accept(Representation) - Method in class net.sourceforge.seqware.queryengine.webservice.view.WorkflowResource

accept.

accessKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

accessKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

accessKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

acquire() - Static method in class net.sourceforge.seqware.pipeline.tools.RunLock

Acquires a lock or throws an unchecked exception if it could not be acquired.

Adag - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object

Adag object match to the element, which is a root element in a dax.

Adag(AbstractWorkflowDataModel) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag

add(Integer, FileAttribute) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService

add.

add(Integer, FileAttribute) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl

add.

add(FileAttribute) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO

add.

add(FileAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate

add.

add(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate

add.

add(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate

add.

add(WorkflowAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO

add.

add(WorkflowRunAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO

add.

add(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentLibraryDesignList

add.

add(Experiment) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList

add.

add(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignList

add.

add(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignReadSpecList

add.

add(File) - Method in class net.sourceforge.seqware.common.model.lists.FileList

add.

add(Integer) - Method in class net.sourceforge.seqware.common.model.lists.IntegerList

add.

add(IUS) - Method in class net.sourceforge.seqware.common.model.lists.IUSList

add.

add(Lane) - Method in class net.sourceforge.seqware.common.model.lists.LaneList

add.

add(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList

add.

add(LibrarySource) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySourceList

add.

add(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList

add.

add(Organism) - Method in class net.sourceforge.seqware.common.model.lists.OrganismList

add.

add(Platform) - Method in class net.sourceforge.seqware.common.model.lists.PlatformList

add.

add(Processing) - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList

add.

add(ReturnValue) - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList

add.

add(Sample) - Method in class net.sourceforge.seqware.common.model.lists.SampleList

add.

add(SequencerRun) - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList

add.

add(Study) - Method in class net.sourceforge.seqware.common.model.lists.StudyList

add.

add(StudyType) - Method in class net.sourceforge.seqware.common.model.lists.StudyTypeList

add.

add(Workflow) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList

add.

add(WorkflowParam) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList

add.

add(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList

add.

add(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList

add.

add(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2

add.

add(Element, String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

add(Element, String, String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

add_empty_processing_event(int[]) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

add_empty_processing_event.

add_empty_processing_event(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

add_empty_processing_event.

add_empty_processing_event(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

add_empty_processing_event.

add_empty_processing_event(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

add_empty_processing_event.

add_empty_processing_event_by_parent_accession(int[]) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

add_empty_processing_event_by_parent_accession.

add_empty_processing_event_by_parent_accession(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

add_empty_processing_event_by_parent_accession.

add_empty_processing_event_by_parent_accession(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

add_empty_processing_event_by_parent_accession.

add_empty_processing_event_by_parent_accession(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

add_empty_processing_event_by_parent_accession.

add_task_group(int[], int[], String, String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

add_task_group.

add_task_group(int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

add_task_group.

add_task_group(int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

add_task_group.

add_task_group(int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

add_task_group.

add_workflow_run(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

add_workflow_run.

add_workflow_run(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

add_workflow_run.

add_workflow_run(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

add_workflow_run.

add_workflow_run(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

add_workflow_run.

add_workflow_run_ancestor(int, int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

add_workflow_run_ancestor.

add_workflow_run_ancestor(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

add_workflow_run_ancestor.

add_workflow_run_ancestor(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

add_workflow_run_ancestor.

add_workflow_run_ancestor(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

add_workflow_run_ancestor.

addArgument(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command

addArgument(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule

addArgument.

addArgumentPair(String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule

addArgumentPair.

addAttribute(AttributeDto) - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource

addAttribute.

addAttribute(AttributeDto) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource

addAttribute.

addAttributeToReturnValue(ReturnValue, String, String) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

addDirectory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

create a user defined directory before all jobs started

addExperiment(Integer, Integer, String, String, Integer, Integer) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

addExperiment.

addExperiment(Integer, Integer, String, String, Integer, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

addExperiment.

addExperiment(Integer, Integer, String, String, Integer, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

addExperiment.

addExperiment(Integer, Integer, String, String, Integer, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

addExperiment.

addExperiment() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

addFile() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

addFile(SqwFile) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

add a job specific file for provision

addFile(SqwFile) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

add a job specific file

addIUS(Integer, Integer, String, String, String, boolean) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

addSample.

addIUS(Integer, Integer, String, String, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

addIUS(Integer, Integer, String, String, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

addIUS(Integer, Integer, String, String, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

addIUS() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

addJobs(AbstractJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow

add job to the workflow

addLane(Integer, Integer, Integer, Integer, Integer, String, String, String, boolean, Integer) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

addSample.

addLane(Integer, Integer, Integer, Integer, Integer, String, String, String, boolean, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

addLane(Integer, Integer, Integer, Integer, Integer, String, String, String, boolean, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

addLane(Integer, Integer, Integer, Integer, Integer, String, String, String, boolean, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

addLane() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

addParent(OozieJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

addParent(PegasusJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

addParent(AbstractJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

add a parent

addParent(Job) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

addParent(Job) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

add job's parent

addParentAccessionFile(String...) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

Return true only when an accession file is added successfully

addParentAccessionFile(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

addProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.Lane

addProcessing.

addProcessings(IUS) - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems

addProcessings.

addProp(Element, String, String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

addQueryParams(ClientResource, Map<?, ? extends List<?>>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel

addRequirement(Requirement) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

addRow(Flexigrid.Cells) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid

addRow.

addSample(Integer, Integer, Integer, String, String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

addSample.

addSample(Integer, Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

addSample.

addSample(Integer, Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

addSample.

addSample(Integer, Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

addSample.

addSample() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

addSequencerRun(Integer, String, String, boolean, boolean, String, SequencerRunStatus) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

addSample.

addSequencerRun(Integer, String, String, boolean, boolean, String, SequencerRunStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

addSequencerRun(Integer, String, String, boolean, boolean, String, SequencerRunStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

addSequencerRun(Integer, String, String, boolean, boolean, String, SequencerRunStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

FIXME: there are problems with setting accession when I should set ID

addSequencerRun() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

addStudy(String, String, String, String, Integer) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

addStudy.

addStudy(String, String, String, String, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

addStudy.

addStudy(String, String, String, String, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

addStudy.

addStudy(String, String, String, String, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

addStudy.

addStudy() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

addTest(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow

add a test command for the workflow

addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean, String, String, String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

addWorkflow.

addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean, String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean, String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

addWorkflow.

addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean, String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

addWorkflow.

addWorkflow() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

addWorkflowRun(String, String, String) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

addWorkflowRun() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

addWorkflowRunParam(int, String, String, String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB

addWorkflowRunParam.

afterUnmarshal(Unmarshaller, Object) - Method in class io.seqware.webservice.generated.model.Processing

algorithm - Variable in class net.sourceforge.seqware.common.module.ReturnValue

algorithmName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

aligned(String) - Static method in class net.sourceforge.seqware.common.util.TabExpansionUtil

Produce aligned output that lines up properly in the terminal

AlignmentQualityReportDecider - Class in net.sourceforge.seqware.pipeline.deciders

FIXME: this extends the plugin but really it should be a decider subclass.

AlignmentQualityReportDecider() - Constructor for class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider

ALL - Static variable in class net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility

AnalisysBulkDownloadListController - Class in net.sourceforge.solexatools.webapp.controller

AnalisysBulkDownloadListController class.

AnalisysBulkDownloadListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController

Constructor for AnalisysBulkDownloadListController.

AnalisysBulkDownloadListDetailsController - Class in net.sourceforge.solexatools.webapp.controller

AnalisysBulkDownloadListDetailsController class.

AnalisysBulkDownloadListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController

Constructor for AnalisysBulkDownloadListDetailsController.

AnalisysEventController - Class in net.sourceforge.solexatools.webapp.controller

StudyController

AnalisysEventController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysEventController

Constructor for AnalisysEventController.

AnalisysEventController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysEventController

Constructor for AnalisysEventController.

AnalisysListController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController

AnalisysListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysListController

Constructor for AnalisysListController.

AnalisysListDetailsController - Class in net.sourceforge.solexatools.webapp.controller

AnalisysListDetailsController class.

AnalisysListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController

Constructor for AnalisysListDetailsController.

AnalisysRunningListDetailsController - Class in net.sourceforge.solexatools.webapp.controller

AnalisysRunningListDetailsController class.

AnalisysRunningListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController

Constructor for AnalisysRunningListDetailsController.

AnalisysTableController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController

AnalisysTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysTableController

Constructor for AnalisysListController.

AnalisysTableControllerDetails - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController

AnalisysTableControllerDetails() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails

Constructor for AnalisysListController.

ANALYSIS_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant

Constant ANALYSIS_VIEW="redirect:/myAnalisysList.htm"

annotateExperiment(int, ExperimentAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateExperiment.

annotateExperiment(int, Set<ExperimentAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateExperiment.

annotateExperiment(int, ExperimentAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateExperiment.

annotateExperiment(int, Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateExperiment.

annotateExperiment(int, ExperimentAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateExperiment.

annotateExperiment(int, Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateExperiment.

annotateExperiment(int, ExperimentAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateExperiment.

annotateExperiment(int, Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateExperiment.

annotateFile(int, FileAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateFile.

annotateFile(int, Set<FileAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateFile.

annotateFile(int, FileAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateFile(int, Set<FileAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateFile(int, FileAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateFile(int, Set<FileAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateFile(int, Set<FileAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateFile.

annotateFile(int, FileAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateFile.

annotateIUS(int, IUSAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateIUS.

annotateIUS(int, Set<IUSAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateIUS.

annotateIUS(int, IUSAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateIUS.

annotateIUS(int, Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateIUS.

annotateIUS(int, IUSAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateIUS.

annotateIUS(int, Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateIUS.

annotateIUS(int, IUSAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateIUS.

annotateIUS(int, Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateIUS.

annotateLane(int, LaneAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateLane.

annotateLane(int, Set<LaneAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateLane.

annotateLane(int, LaneAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateLane.

annotateLane(int, Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateLane.

annotateLane(int, LaneAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateLane.

annotateLane(int, Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateLane.

annotateLane(int, LaneAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateLane.

annotateLane(int, Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateLane.

annotateProcessing(int, ProcessingAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateProcessing.

annotateProcessing(int, Set<ProcessingAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateProcessing.

annotateProcessing(int, ProcessingAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateProcessing.

annotateProcessing(int, Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateProcessing.

annotateProcessing(int, ProcessingAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateProcessing.

annotateProcessing(int, Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateProcessing.

annotateProcessing(int, ProcessingAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateProcessing.

annotateProcessing(int, Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateProcessing.

annotateSample(int, SampleAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateSample.

annotateSample(int, Set<SampleAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateSample.

annotateSample(int, SampleAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateSample.

annotateSample(int, Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateSample.

annotateSample(int, SampleAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateSample.

annotateSample(int, Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateSample.

annotateSample(int, SampleAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateSample.

annotateSample(int, Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateSample.

annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateSequencerRun.

annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateSequencerRun.

annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateSequencerRun.

annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateSequencerRun.

annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateSequencerRun.

annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateSequencerRun.

annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateSequencerRun.

annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateSequencerRun.

annotateStudy(int, StudyAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateStudy.

annotateStudy(int, Set<StudyAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateStudy.

annotateStudy(int, StudyAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateStudy.

annotateStudy(int, Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateStudy.

annotateStudy(int, StudyAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateStudy.

annotateStudy(int, Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateStudy.

annotateStudy(int, StudyAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateStudy.

annotateStudy(int, Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateStudy.

annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateWorkflow.

annotateWorkflow(int, Set<WorkflowAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateWorkflow.

annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateWorkflow.

annotateWorkflow(int, Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateWorkflow.

annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateWorkflow.

annotateWorkflow(int, Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateWorkflow.

annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateWorkflow.

annotateWorkflow(int, Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateWorkflow.

annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateWorkflowRun.

annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

annotateWorkflowRun.

annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateWorkflowRun.

annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

annotateWorkflowRun.

annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateWorkflowRun.

annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

annotateWorkflowRun.

annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateWorkflowRun.

annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

annotateWorkflowRun.

appID - Variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

appID - Static variable in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker

Argument - Class in net.sourceforge.seqware.pipeline.workflowV2.model

Argument class.

Argument(String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Argument

Constructor for Argument.

asDto(SampleSearch) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos

asDto.

asDto(Attribute) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos

asDto.

asDto(Registration) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos

asDto.

asDto(Sample) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos

asDto.

asDto(IUS) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos

asDto.

asDto(File) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos

asDto.

associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

associate_processing_event_with_parents_and_child.

associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

associate_processing_event_with_parents_and_child.

associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

associate_processing_event_with_parents_and_child.

associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

associate_processing_event_with_parents_and_child.

atDto(Organism) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos

atDto.

attachAndIterateBuckets(OozieProvisionFileJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp.BucketGenerator

Creates new buckets as needed when provisionjobs are added

attachJob(OozieBashJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieBashJob

attachProvisionFileJob(OozieProvisionFileJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieProvisionFileJob

Attribute<T> - Interface in net.sourceforge.seqware.common.model

Attribute interface.

attribute - Variable in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource

AttributeAnnotator - Class in net.sourceforge.seqware.pipeline.plugins

AttributeAnnotator class.

AttributeAnnotator() - Constructor for class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator

Constructor for AttributeAnnotator.

AttributeDto - Class in net.sourceforge.seqware.webservice.dto

AttributeDto() - Constructor for class net.sourceforge.seqware.webservice.dto.AttributeDto

AttributePlugin - Class in net.sourceforge.seqware.pipeline.plugins.checkdb.plugins

Checks the metadb for issues with attributes.

AttributePlugin() - Constructor for class net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.AttributePlugin

attributes - Variable in class net.sourceforge.seqware.common.module.ReturnValue

authenticate() - Method in class net.sourceforge.seqware.webservice.resources.BasicResource

authenticate.

authenticate(String) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet

authenticate.

Authentication - Class in net.sourceforge.solexatools.authentication

Abstract Authentication class.

Authentication() - Constructor for class net.sourceforge.solexatools.authentication.Authentication

B

BadFile - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode

Constant BadFile=3

BadModule - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode

Constant BadModule=4

BadParameter - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode

Constant BadParameter=2

BadRunnerParams - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode

Constant BadRunnerParams=5

basedir - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

BashJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model

BashJob(String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.BashJob

BASIC_TEST_DB_HOST_KEY - Static variable in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator

BASIC_TEST_DB_NAME_KEY - Static variable in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator

BASIC_TEST_PASSWORD_KEY - Static variable in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator

BASIC_TEST_USERNAME_KEY - Static variable in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator

BasicDecider - Class in net.sourceforge.seqware.pipeline.deciders

BasicDecider() - Constructor for class net.sourceforge.seqware.pipeline.deciders.BasicDecider

BasicDecider.FILE_STATUS - Enum in net.sourceforge.seqware.pipeline.deciders

These file statuses reflect the discussion at https://wiki.oicr.on.ca/display/SEQWARE/BasicDecider+logic

BasicDecider.PREVIOUS_RUN_STATUS - Enum in net.sourceforge.seqware.pipeline.deciders

We care about three types of status, an outright fail, other (pending, running, submitted, etc.), and completed

basicResetDatabaseWithUsers() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

Unfortunately, postgres does not allow the straight dropdb and createdb when tomcat is used (perhaps we leave open a connection)

BasicResource - Class in net.sourceforge.seqware.webservice.resources

See https://sourceforge.net/apps/mediawiki/seqware/index.php?title=How_to_extend_the_web_service#Basic_Resource

BasicResource() - Constructor for class net.sourceforge.seqware.webservice.resources.BasicResource

Constructor for BasicResource.

BasicRestlet - Class in net.sourceforge.seqware.webservice.resources

See https://sourceforge.net/apps/mediawiki/seqware/index.php?title=How_to_extend_the_web_service#Basic_Resource

BasicRestlet(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.BasicRestlet

Constructor for BasicRestlet.

BasicTestDatabaseCreator - Class in net.sourceforge.seqware.common.util.testtools

This class controls configuration of the database used for integration tests.

BasicTestDatabaseCreator() - Constructor for class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator

BasicTestDatabaseCreatorWrapper - Class in net.sourceforge.seqware.common.util.testtools

BasicTestDatabaseCreatorWrapper class.

BasicTestDatabaseCreatorWrapper() - Constructor for class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreatorWrapper

BasicWorkflow - Class in net.sourceforge.seqware.pipeline.workflow

Abstract BasicWorkflow class.

BasicWorkflow(Metadata, Map<String, String>) - Constructor for class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

Constructor for BasicWorkflow.

BasicWorkflow.Job - Enum in net.sourceforge.seqware.pipeline.workflow

BatchedOozieBashJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object

Container for batching up jobs

BatchedOozieBashJob(AbstractJob, String, String, boolean, File, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieBashJob

BatchedOozieProvisionFileJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object

Container for batching up provision file jobs

BatchedOozieProvisionFileJob(AbstractJob, String, String, boolean, File, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieProvisionFileJob

BatchMetadataInjection - Class in net.sourceforge.seqware.pipeline.plugins

BatchImport class.

BatchMetadataInjection() - Constructor for class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection

Constructor for AttributeAnnotator.

BatchMetadataParser - Class in net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection

BatchMetadataParser(Metadata, Map<String, String>, boolean) - Constructor for class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

BatchMetadataParser.Field - Enum in net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection

BeanFactory - Class in net.sourceforge.seqware.common.factory

Abstract BeanFactory class.

BeanFactory() - Constructor for class net.sourceforge.seqware.common.factory.BeanFactory

bind(HttpServletRequest, Object) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

bindSessionToThread() - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions

bindSessionToThread.

bindSessionToThread(FlushMode) - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions

bindSessionToThread.

Bool - Class in net.sourceforge.seqware.common.util

Bool() - Constructor for class net.sourceforge.seqware.common.util.Bool

BUCKET_SIZE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp

BufferedReaderThread - Class in net.sourceforge.seqware.common.util.iotools

BufferedReaderThread class.

BufferedReaderThread(InputStream) - Constructor for class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread

Constructor for BufferedReaderThread.

BufferedReaderThread(InputStream, int) - Constructor for class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread

Constructor for BufferedReaderThread.

BUFFERSIZE - Static variable in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController

Constant BUFFERSIZE=500*1024

buildCommandString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJavaJob

buildCommandString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

for overridden by a specific job type

buildCommandString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusPerlJob

buildCommandString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob

buildDirectory(File) - Static method in class net.sourceforge.solexatools.util.ZipFileUtil

buildDirectory.

buildMetadataString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

buildWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

to be Overridden by the workflow author

buildWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.XmlWorkflowDataModel

BulkDownloaderController - Class in net.sourceforge.solexatools.webapp.controller

BulkDownloaderController class.

BulkDownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController

Constructor for BulkDownloaderController.

BulkDownloaderSizeValidatorController - Class in net.sourceforge.solexatools.webapp.controller

BulkDownloaderSizeValidatorController class.

BulkDownloaderSizeValidatorController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloaderSizeValidatorController

BulkDownloadListController - Class in net.sourceforge.solexatools.webapp.controller

BulkDownloadListController class.

BulkDownloadListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController

Constructor for BulkDownloadListController.

BulkDownloadListDetailsController - Class in net.sourceforge.solexatools.webapp.controller

BulkDownloadListDetailsController class.

BulkDownloadListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Constructor for BulkDownloadListDetailsController.

BulkUtil - Class in net.sourceforge.solexatools.util

BulkUtil class.

BulkUtil() - Constructor for class net.sourceforge.solexatools.util.BulkUtil

Bundle - Class in net.sourceforge.seqware.pipeline.bundle

This is a utility class that lets you manipulate a workflow bundle.

Bundle() - Constructor for class net.sourceforge.seqware.pipeline.bundle.Bundle

Constructor for Bundle.

Bundle(Metadata, Map<String, String>) - Constructor for class net.sourceforge.seqware.pipeline.bundle.Bundle

Constructor for Bundle.

bundleDir - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle

BundleDir_Check - Class in io.seqware.pipeline.plugins.sanity.checks

BundleDir_Check() - Constructor for class io.seqware.pipeline.plugins.sanity.checks.BundleDir_Check

BundleInfo - Class in net.sourceforge.seqware.pipeline.bundle

BundleInfo class.

BundleInfo() - Constructor for class net.sourceforge.seqware.pipeline.bundle.BundleInfo

BundleManager - Class in net.sourceforge.seqware.pipeline.plugins

BundleManager class.

BundleManager() - Constructor for class net.sourceforge.seqware.pipeline.plugins.BundleManager

Constructor for BundleManager.

bundleUtil - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

byte2HexString(byte[]) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

byte2HexString.

C

calculateTotalTime(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport

calculateTotalTime.

CancelAnalysisWorkflowController - Class in net.sourceforge.solexatools.webapp.controller

CancelAnalysisWorkflowController class.

CancelAnalysisWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController

Constructor for CancelAnalysisWorkflowController.

CancelBulkDownloaderController - Class in net.sourceforge.solexatools.webapp.controller

CancelBulkDownloaderController class.

CancelBulkDownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.CancelBulkDownloaderController

Constructor for CancelBulkDownloaderController.

CancelInputDownloaderController - Class in net.sourceforge.solexatools.webapp.controller

CancelInputDownloaderController class.

CancelInputDownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.CancelInputDownloaderController

Constructor for CancelInputDownloaderController.

causedBy(Throwable, Class) - Static method in class net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools

causedBy.

ChangeNumberPopupPageController - Class in net.sourceforge.solexatools.webapp.controller

ChangeNumberPopupPageController class.

ChangeNumberPopupPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController

Constructor for ChangeNumberPopupPageController.

ChangeWorkflowParamValueController - Class in net.sourceforge.solexatools.webapp.controller

ChangeWorkflowParamValueController class.

ChangeWorkflowParamValueController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController

Constructor for ChangeWorkflowParamValueController.

check(QueryRunner, Metadata) - Method in class io.seqware.pipeline.plugins.sanity.checks.BundleDir_Check

check(QueryRunner, Metadata) - Method in class io.seqware.pipeline.plugins.sanity.checks.CLICheck

check(QueryRunner, Metadata) - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_Check

check(QueryRunner, Metadata) - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_WS_ConsistencyCheck

check(QueryRunner, Metadata) - Method in class io.seqware.pipeline.plugins.sanity.checks.HDFS_Check

check(QueryRunner, Metadata) - Method in class io.seqware.pipeline.plugins.sanity.checks.Oozie_Check

check(QueryRunner, Metadata) - Method in class io.seqware.pipeline.plugins.sanity.checks.Script_Check

check(QueryRunner, Metadata) - Method in class io.seqware.pipeline.plugins.sanity.checks.TutorialCheck

check(QueryRunner, Metadata) - Method in class io.seqware.pipeline.plugins.sanity.checks.WS_Check

check(QueryRunner, Metadata) - Method in interface io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface

check(SelectQueryRunner, SortedMap<CheckDBPluginInterface.Level, Set<String>>) - Method in interface net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDBPluginInterface

check(SelectQueryRunner, SortedMap<CheckDBPluginInterface.Level, Set<String>>) - Method in class net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.AttributePlugin

check(SelectQueryRunner, SortedMap<CheckDBPluginInterface.Level, Set<String>>) - Method in class net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.OrphanCheckerPlugin

check(SelectQueryRunner, SortedMap<CheckDBPluginInterface.Level, Set<String>>) - Method in class net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.SampleHierarchyPlugin

check(SelectQueryRunner, SortedMap<CheckDBPluginInterface.Level, Set<String>>) - Method in class net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.WorkflowRunConventionsPlugin

CHECK - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant CHECK="check"

CHECK - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController

Constant CHECK="check"

CheckDB - Class in net.sourceforge.seqware.pipeline.plugins.checkdb

A database validation tool for your SeqWare metadb

CheckDB() - Constructor for class net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB

Constructor for HelloWorld.

CheckDBPluginInterface - Interface in net.sourceforge.seqware.pipeline.plugins.checkdb

Specifies an interface for database checks that can be run against the seqware database

CheckDBPluginInterface.Level - Enum in net.sourceforge.seqware.pipeline.plugins.checkdb

checkExit(int) - Method in class net.sourceforge.seqware.common.util.NoExitSecurityManager

checkFields(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

checkFileDetails(ReturnValue, FileMetadata) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

Performs any additional checks on the file before adding it to the list of files to incorporate.

CheckForCycles - Class in net.sourceforge.seqware.common.hibernate

CheckForCycles class.

CheckForCycles() - Constructor for class net.sourceforge.seqware.common.hibernate.CheckForCycles

checkForValidOptions(OptionSet) - Static method in class net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility

checkPermission(Permission) - Method in class net.sourceforge.seqware.common.util.NoExitSecurityManager

checkPermission(Permission, Object) - Method in class net.sourceforge.seqware.common.util.NoExitSecurityManager

checkProcessing(Processing) - Method in class net.sourceforge.seqware.common.hibernate.CheckForCycles

checkProcessing.

checkSample(Sample) - Method in class net.sourceforge.seqware.common.hibernate.CheckForCycles

checkSample.

checkStudy(Integer) - Method in class net.sourceforge.seqware.common.hibernate.CheckForCycles

checkStudy.

children - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

choiceOf(String, String, String[], String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

Handles prompting for a choice out of a list of choices using integers.

clean_up() - Method in class io.seqware.pipeline.plugins.sanity.SanityCheck

clean_up() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

clean_up.

clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

clean_up.

clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

clean_up.

clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

clean_up.

clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel

clean_up() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

clean_up() - Method in class net.sourceforge.seqware.pipeline.module.Module

clean_up.

clean_up() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

clean_up.

clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver

Deprecated.

clean_up.

clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

clean_up.

clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

clean_up.

clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

clean_up.

clean_up() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.deletion.DeletionDB

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.fileprovenance.FileProvenanceReporter

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter

Perform post-task clean-up here.

clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker

Perform post-task clean-up here.

cli2Map(String[], Map<String, String>) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools

Method to getValues all "--key=value" or "--key value" parameters and add them to hashmap

CLICheck - Class in io.seqware.pipeline.plugins.sanity.checks

Runs through our CLI tutorial

CLICheck() - Constructor for class io.seqware.pipeline.plugins.sanity.checks.CLICheck

clone(Processing) - Static method in class net.sourceforge.seqware.common.model.Processing

clone.

clone() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

clone() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

cloneToHibernate(Processing) - Static method in class net.sourceforge.seqware.common.model.Processing

cloneToHibernate.

cloneToHibernate(WorkflowRun) - Static method in class net.sourceforge.seqware.common.model.WorkflowRun

cloneToHibernate.

close() - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

close() - Static method in class net.sourceforge.seqware.common.factory.DBAccess

close.

closeBufferWriter() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

collectProcessingList(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDProcessingsResource

collectProcessingList.

collectProcessings(WorkflowRun) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport

Command - Class in net.sourceforge.seqware.pipeline.workflowV2.model

Command() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Command

commaSeparateMy(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

compare(ExperimentSpotDesignReadSpec, ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.model.comparator.ExperimentSpotDesignReadSpecComparator

compare(ModuleInterface, ModuleInterface) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.ModuleComparator

compare(PluginInterface, PluginInterface) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.PluginComparator

compareTo(ModelAccessionIDTuple) - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple

compareTo(ModelAccessionIDTuple) - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple

compareTo(SequencerRunReport.Row) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

compareTo(Expense) - Method in class net.sourceforge.seqware.common.model.Expense

compareTo(Experiment) - Method in class net.sourceforge.seqware.common.model.Experiment

compareTo(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

compareTo(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

compareTo.

compareTo(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

compareTo.

compareTo(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

compareTo(File) - Method in class net.sourceforge.seqware.common.model.File

compareTo(FileAttribute) - Method in class net.sourceforge.seqware.common.model.FileAttribute

compareTo(FileType) - Method in class net.sourceforge.seqware.common.model.FileType

compareTo(Invoice) - Method in class net.sourceforge.seqware.common.model.Invoice

compareTo(IUS) - Method in class net.sourceforge.seqware.common.model.IUS

compareTo(IUSAttribute) - Method in class net.sourceforge.seqware.common.model.IUSAttribute

compareTo(Lane) - Method in class net.sourceforge.seqware.common.model.Lane

compareTo(LaneAttribute) - Method in class net.sourceforge.seqware.common.model.LaneAttribute

compareTo(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.LibrarySelection

compareTo(LibrarySource) - Method in class net.sourceforge.seqware.common.model.LibrarySource

compareTo(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy

compareTo(Organism) - Method in class net.sourceforge.seqware.common.model.Organism

compareTo(Platform) - Method in class net.sourceforge.seqware.common.model.Platform

compareTo(Processing) - Method in class net.sourceforge.seqware.common.model.Processing

compareTo(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

compareTo(Registration) - Method in class net.sourceforge.seqware.common.model.Registration

compareTo(Sample) - Method in class net.sourceforge.seqware.common.model.Sample

compareTo(SampleAttribute) - Method in class net.sourceforge.seqware.common.model.SampleAttribute

compareTo(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SequencerRun

compareTo(SequencerRunAttribute) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

compareTo(ShareStudy) - Method in class net.sourceforge.seqware.common.model.ShareStudy

compareTo(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

compareTo(Study) - Method in class net.sourceforge.seqware.common.model.Study

compareTo.

compareTo(StudyAttribute) - Method in class net.sourceforge.seqware.common.model.StudyAttribute

compareTo(StudyType) - Method in class net.sourceforge.seqware.common.model.StudyType

compareTo.

compareTo(Workflow) - Method in class net.sourceforge.seqware.common.model.Workflow

compareTo(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute

compareTo(WorkflowParam) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

compareTo(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

compareTo(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

compareTo.

compareTo(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

compareTo(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute

compareTo(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

compareTo(LaneInfo) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

compareTo(SampleInfo) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

compareTo(TagValueUnit) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit

compareTo(StudySampleReportFileLineItem) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

compareTo(StudySampleReportLineItem) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

compareWorkflowRunFiles(Set<Integer>, Collection<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

Tests if the files from the workflow run (filesHasRun) are the same as those found in the database (filesToRun).

COMPRESSION_SETTING - Static variable in class net.sourceforge.seqware.common.util.filetools.FileTools

concat(String, List<String>) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

config - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle

config - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin

config - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

configs - Variable in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

ConfigTools - Class in net.sourceforge.seqware.common.util.configtools

ConfigTools class.

ConfigTools() - Constructor for class net.sourceforge.seqware.common.util.configtools.ConfigTools

configureFileProvenanceParams(OptionParser) - Static method in class net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility

ConsoleAdapter - Class in net.sourceforge.seqware.common.util.runtools

ConsoleAdapter() - Constructor for class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

CONST_AT_SIGN - Static variable in class net.sourceforge.solexatools.validation.LoginValidator

Constant CONST_AT_SIGN="@"

Constant - Class in net.sourceforge.solexatools.util

Constant class.

Constant() - Constructor for class net.sourceforge.solexatools.util.Constant

constructCommand() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

ContextImpl - Class in net.sourceforge.seqware.common

ContextImpl class.

ControllerUtil - Class in net.sourceforge.solexatools.util

ControllerUtil class.

ControllerUtil() - Constructor for class net.sourceforge.solexatools.util.ControllerUtil

convertOptionsToMap(OptionSet, Metadata) - Static method in class net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility

copyBundle(String, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

copyBundle.

copyBundleToS3(File, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

copyBundleToS3.

copyFromLocal(FileSystem, String, Path) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine

copyInputStream(InputStream, OutputStream) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

copyInputStream.

copyInputStream(InputStream, OutputStream) - Static method in class net.sourceforge.solexatools.util.ZipFileUtil

copyInputStream.

copyProperty(Object, String, Object) - Method in class net.sourceforge.seqware.common.util.NullBeanUtils

copyToFile(BufferedInputStream, String, int, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

copyToFile(BufferedInputStream, String, boolean, int, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Copy reader into output.

copyToFile(BufferedInputStream, String, boolean, int, String, Cipher, Cipher) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Copy reader into output using Cipher.

count() - Method in class io.seqware.webservice.generated.controller.AbstractFacade

countOfRows(Study) - Method in interface net.sourceforge.seqware.common.business.FileReportService

countOfRows.

countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.FileReportService

countOfRows.

countOfRows(Study) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl

countOfRows.

countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl

countOfRows.

countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

countOfRows.

countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

countOfRows.

countOfRows(Study) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO

countOfRows.

countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO

countOfRows.

countOfRows(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate

countOfRows.

countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate

countOfRows.

countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

countOfRows.

countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

countOfRows.

countOfStatus(Study, SampleReportService.Status) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

countOfStatus.

countOfStatus(SequencerRun, SampleReportService.Status) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

countOfStatus.

countOfStatus(Study, Workflow, SampleReportService.Status) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

countOfStatus.

countOfStatus(SequencerRun, Workflow, SampleReportService.Status) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

countOfStatus.

countOfStatus(Study, SampleReportService.Status) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

countOfStatus.

countOfStatus(Study, Workflow, SampleReportService.Status) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

countOfStatus.

countOfStatus(SequencerRun, SampleReportService.Status) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

countOfStatus.

countOfStatus(SequencerRun, Workflow, SampleReportService.Status) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

countOfStatus.

countOfStatus(Study, SampleReportService.Status) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

countOfStatus.

countOfStatus(Study, Workflow, SampleReportService.Status) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

countOfStatus.

countOfStatus(SequencerRun, Workflow, SampleReportService.Status) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

countOfStatus.

countOfStatus(SequencerRun, SampleReportService.Status) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

countOfStatus.

countOfStatus(Study, SampleReportService.Status) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

countOfStatus.

countOfStatus(SequencerRun, SampleReportService.Status) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

countOfStatus.

countOfStatus(Study, Workflow, SampleReportService.Status) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

countOfStatus.

countOfStatus(SequencerRun, Workflow, SampleReportService.Status) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

countOfStatus.

countREST() - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

countREST() - Method in class io.seqware.webservice.generated.controller.ExpenseAttributeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ExpenseFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ExperimentAttributeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ExperimentFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ExperimentLibraryDesignFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ExperimentLinkFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignReadSpecFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.FileAttributeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.FileFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.FileReportFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.FileTypeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.InvoiceAttributeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.InvoiceFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.IusAttributeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.IusFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.IusLinkFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.IusWorkflowRunsFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.LaneAttributeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.LaneFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.LaneLinkFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.LaneTypeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.LaneWorkflowRunsFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.LibrarySelectionFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.LibrarySourceFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.LibraryStrategyFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.OrganismFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.PlatformFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ProcessingAttributeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ProcessingExperimentsFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ProcessingFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ProcessingFilesFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ProcessingIusFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ProcessingLanesFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ProcessingRelationshipFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ProcessingSamplesFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ProcessingSequencerRunsFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ProcessingStudiesFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.RegistrationFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.SampleAttributeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.SampleFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.SampleLinkFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.SampleRelationshipFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.SampleReportFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.SampleSearchAttributeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.SampleSearchFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.SequencerRunAttributeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.SequencerRunFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ShareExperimentFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ShareFileFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ShareLaneFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ShareProcessingFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ShareSampleFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ShareStudyFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.ShareWorkflowRunFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.StudyAttributeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.StudyFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.StudyLinkFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.StudyTypeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.WorkflowAttributeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.WorkflowFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.WorkflowParamFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.WorkflowParamValueFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.WorkflowRunAttributeFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.WorkflowRunFacadeREST

countREST() - Method in class io.seqware.webservice.generated.controller.WorkflowRunParamFacadeREST

create(T) - Method in class io.seqware.webservice.generated.controller.AbstractFacade

create(ExpenseAttribute) - Method in class io.seqware.webservice.generated.controller.ExpenseAttributeFacadeREST

create(Expense) - Method in class io.seqware.webservice.generated.controller.ExpenseFacadeREST

create(ExperimentAttribute) - Method in class io.seqware.webservice.generated.controller.ExperimentAttributeFacadeREST

create(Experiment) - Method in class io.seqware.webservice.generated.controller.ExperimentFacadeREST

create(ExperimentLibraryDesign) - Method in class io.seqware.webservice.generated.controller.ExperimentLibraryDesignFacadeREST

create(ExperimentLink) - Method in class io.seqware.webservice.generated.controller.ExperimentLinkFacadeREST

create(ExperimentSpotDesign) - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignFacadeREST

create(ExperimentSpotDesignReadSpec) - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignReadSpecFacadeREST

create(FileAttribute) - Method in class io.seqware.webservice.generated.controller.FileAttributeFacadeREST

create(File) - Method in class io.seqware.webservice.generated.controller.FileFacadeREST

create(FileReport) - Method in class io.seqware.webservice.generated.controller.FileReportFacadeREST

create(FileType) - Method in class io.seqware.webservice.generated.controller.FileTypeFacadeREST

create(InvoiceAttribute) - Method in class io.seqware.webservice.generated.controller.InvoiceAttributeFacadeREST

create(Invoice) - Method in class io.seqware.webservice.generated.controller.InvoiceFacadeREST

create(IusAttribute) - Method in class io.seqware.webservice.generated.controller.IusAttributeFacadeREST

create(Ius) - Method in class io.seqware.webservice.generated.controller.IusFacadeREST

create(IusLink) - Method in class io.seqware.webservice.generated.controller.IusLinkFacadeREST

create(IusWorkflowRuns) - Method in class io.seqware.webservice.generated.controller.IusWorkflowRunsFacadeREST

create(LaneAttribute) - Method in class io.seqware.webservice.generated.controller.LaneAttributeFacadeREST

create(Lane) - Method in class io.seqware.webservice.generated.controller.LaneFacadeREST

create(LaneLink) - Method in class io.seqware.webservice.generated.controller.LaneLinkFacadeREST

create(LaneType) - Method in class io.seqware.webservice.generated.controller.LaneTypeFacadeREST

create(LaneWorkflowRuns) - Method in class io.seqware.webservice.generated.controller.LaneWorkflowRunsFacadeREST

create(LibrarySelection) - Method in class io.seqware.webservice.generated.controller.LibrarySelectionFacadeREST

create(LibrarySource) - Method in class io.seqware.webservice.generated.controller.LibrarySourceFacadeREST

create(LibraryStrategy) - Method in class io.seqware.webservice.generated.controller.LibraryStrategyFacadeREST

create(Organism) - Method in class io.seqware.webservice.generated.controller.OrganismFacadeREST

create(Platform) - Method in class io.seqware.webservice.generated.controller.PlatformFacadeREST

create(ProcessingAttribute) - Method in class io.seqware.webservice.generated.controller.ProcessingAttributeFacadeREST

create(ProcessingExperiments) - Method in class io.seqware.webservice.generated.controller.ProcessingExperimentsFacadeREST

create(Processing) - Method in class io.seqware.webservice.generated.controller.ProcessingFacadeREST

create(ProcessingFiles) - Method in class io.seqware.webservice.generated.controller.ProcessingFilesFacadeREST

create(ProcessingIus) - Method in class io.seqware.webservice.generated.controller.ProcessingIusFacadeREST

create(ProcessingLanes) - Method in class io.seqware.webservice.generated.controller.ProcessingLanesFacadeREST

create(ProcessingRelationship) - Method in class io.seqware.webservice.generated.controller.ProcessingRelationshipFacadeREST

create(ProcessingSamples) - Method in class io.seqware.webservice.generated.controller.ProcessingSamplesFacadeREST

create(ProcessingSequencerRuns) - Method in class io.seqware.webservice.generated.controller.ProcessingSequencerRunsFacadeREST

create(ProcessingStudies) - Method in class io.seqware.webservice.generated.controller.ProcessingStudiesFacadeREST

create(Registration) - Method in class io.seqware.webservice.generated.controller.RegistrationFacadeREST

create(SampleAttribute) - Method in class io.seqware.webservice.generated.controller.SampleAttributeFacadeREST

create(Sample) - Method in class io.seqware.webservice.generated.controller.SampleFacadeREST

create(SampleLink) - Method in class io.seqware.webservice.generated.controller.SampleLinkFacadeREST

create(SampleRelationship) - Method in class io.seqware.webservice.generated.controller.SampleRelationshipFacadeREST

create(SampleReport) - Method in class io.seqware.webservice.generated.controller.SampleReportFacadeREST

create(SampleSearchAttribute) - Method in class io.seqware.webservice.generated.controller.SampleSearchAttributeFacadeREST

create(SampleSearch) - Method in class io.seqware.webservice.generated.controller.SampleSearchFacadeREST

create(SequencerRunAttribute) - Method in class io.seqware.webservice.generated.controller.SequencerRunAttributeFacadeREST

create(SequencerRun) - Method in class io.seqware.webservice.generated.controller.SequencerRunFacadeREST

create(ShareExperiment) - Method in class io.seqware.webservice.generated.controller.ShareExperimentFacadeREST

create(ShareFile) - Method in class io.seqware.webservice.generated.controller.ShareFileFacadeREST

create(ShareLane) - Method in class io.seqware.webservice.generated.controller.ShareLaneFacadeREST

create(ShareProcessing) - Method in class io.seqware.webservice.generated.controller.ShareProcessingFacadeREST

create(ShareSample) - Method in class io.seqware.webservice.generated.controller.ShareSampleFacadeREST

create(ShareStudy) - Method in class io.seqware.webservice.generated.controller.ShareStudyFacadeREST

create(ShareWorkflowRun) - Method in class io.seqware.webservice.generated.controller.ShareWorkflowRunFacadeREST

create(StudyAttribute) - Method in class io.seqware.webservice.generated.controller.StudyAttributeFacadeREST

create(Study) - Method in class io.seqware.webservice.generated.controller.StudyFacadeREST

create(StudyLink) - Method in class io.seqware.webservice.generated.controller.StudyLinkFacadeREST

create(StudyType) - Method in class io.seqware.webservice.generated.controller.StudyTypeFacadeREST

create(WorkflowAttribute) - Method in class io.seqware.webservice.generated.controller.WorkflowAttributeFacadeREST

create(Workflow) - Method in class io.seqware.webservice.generated.controller.WorkflowFacadeREST

create(WorkflowParam) - Method in class io.seqware.webservice.generated.controller.WorkflowParamFacadeREST

create(WorkflowParamValue) - Method in class io.seqware.webservice.generated.controller.WorkflowParamValueFacadeREST

create(WorkflowRunAttribute) - Method in class io.seqware.webservice.generated.controller.WorkflowRunAttributeFacadeREST

create(WorkflowRun) - Method in class io.seqware.webservice.generated.controller.WorkflowRunFacadeREST

create(WorkflowRunParam) - Method in class io.seqware.webservice.generated.controller.WorkflowRunParamFacadeREST

create(SampleSearch) - Method in class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl

create.

create(SampleSearch) - Method in interface net.sourceforge.seqware.common.business.SampleSearchService

create.

create(SampleSearch) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate

create.

create(SampleSearch) - Method in interface net.sourceforge.seqware.common.dao.SampleSearchDAO

create.

create() - Static method in class net.sourceforge.seqware.common.util.testtools.JndiDatasourceCreator

create.

create_JSON(Object) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

create_XML(Object) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

createBashJob(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

createBashJob(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow

createDatabase() - Static method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreatorWrapper

createDatabase.

createDatabase() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

createDatabase.

createDirectoryWithUniqueName(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

createDirectoryWithUniqueName.

createFile(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

create a sqwfile

createFileWithUniqueName(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

createFileWithUniqueName.

CreateFromScratch - Class in net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection

CreateFromScratch(Metadata, Map<String, String>, boolean) - Constructor for class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.CreateFromScratch

createInboundRoot() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication

Creates a root Restlet that will receive all incoming calls.

createInboundRoot() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion

Creates a root Restlet that will receive all incoming calls.

createINI(HashMap<String, String>) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager

createINI.

createJavaElement() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieBashJob

createJavaElement() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieProvisionFileJob

createJavaElement() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob

createJavaElement() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

createJavaElement() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob

createJavaJob(String, String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow

createJavaSeqwareModuleJob(String, String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow

createJobBatch(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow

createPathToJava() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

createPerlJob(String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow

createSgeElement() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieBashJob

createSgeElement() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieProvisionFileJob

createSgeElement() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob

createSgeElement() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

createSgeElement() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob

createSymlink(String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

createSymlink(String, boolean, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Creates symlink of input to output.

createTargetDirectory(String, String) - Static method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Creates abstract pathname.

createTargetPath(String, String, String) - Static method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Creates abstract pathname.

createTempDirectory(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

createTempDirectory.

createWithBaseEntity(LaneAttribute) - Method in class io.seqware.webservice.controller.CustomLaneAttributeFacadeREST

Create a new lane and a new lane attribute to associate with it in a single step.

createWithBaseEntity(SampleAttribute) - Method in class io.seqware.webservice.controller.CustomSampleAttributeFacadeREST

Create a new sample and a new sample attribute to associate with it in a single step.

createWithBaseEntity(SequencerRunAttribute) - Method in class io.seqware.webservice.controller.CustomSequencerRunAttributeFacadeREST

Create a new sequencer run and a new sequencer run attribute to associate with it in a single step.

createWithBaseEntity(StudyAttribute) - Method in class io.seqware.webservice.controller.CustomStudyAttributeFacadeREST

Create a new study and a new study attribute to associate with it in a single step.

createWorkflow() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

createWorkflowRunParameters(HashMap<String, String>) - Static method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager

CSV_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant CSV_TYPE="csvtype"

CSV_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController

Constant CSV_TYPE="csvtype"

currentBucketCount - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp.BucketGenerator

currStep - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools

currStep - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

CustomExpenseAttributeFacadeREST - Class in io.seqware.webservice.controller

CustomExpenseAttributeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomExpenseAttributeFacadeREST

CustomExpenseFacadeREST - Class in io.seqware.webservice.controller

CustomExpenseFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomExpenseFacadeREST

CustomExperimentAttributeFacadeREST - Class in io.seqware.webservice.controller

CustomExperimentAttributeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomExperimentAttributeFacadeREST

CustomExperimentFacadeREST - Class in io.seqware.webservice.controller

CustomExperimentFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomExperimentFacadeREST

CustomExperimentLibraryDesignFacadeREST - Class in io.seqware.webservice.controller

CustomExperimentLibraryDesignFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomExperimentLibraryDesignFacadeREST

CustomExperimentLinkFacadeREST - Class in io.seqware.webservice.controller

CustomExperimentLinkFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomExperimentLinkFacadeREST

CustomExperimentSpotDesignFacadeREST - Class in io.seqware.webservice.controller

CustomExperimentSpotDesignFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomExperimentSpotDesignFacadeREST

CustomExperimentSpotDesignReadSpecFacadeREST - Class in io.seqware.webservice.controller

CustomExperimentSpotDesignReadSpecFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomExperimentSpotDesignReadSpecFacadeREST

CustomFileAttributeFacadeREST - Class in io.seqware.webservice.controller

CustomFileAttributeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomFileAttributeFacadeREST

CustomFileFacadeREST - Class in io.seqware.webservice.controller

CustomFileFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomFileFacadeREST

CustomFileReportFacadeREST - Class in io.seqware.webservice.controller

CustomFileReportFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomFileReportFacadeREST

CustomFileTypeFacadeREST - Class in io.seqware.webservice.controller

CustomFileTypeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomFileTypeFacadeREST

CustomIntegerEditor - Class in net.sourceforge.solexatools.validation

CustomIntegerEditor class.

CustomIntegerEditor() - Constructor for class net.sourceforge.solexatools.validation.CustomIntegerEditor

Constructor for CustomIntegerEditor.

CustomInvoiceAttributeFacadeREST - Class in io.seqware.webservice.controller

CustomInvoiceAttributeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomInvoiceAttributeFacadeREST

CustomInvoiceFacadeREST - Class in io.seqware.webservice.controller

CustomInvoiceFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomInvoiceFacadeREST

CustomIusAttributeFacadeREST - Class in io.seqware.webservice.controller

CustomIusAttributeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomIusAttributeFacadeREST

CustomIusFacadeREST - Class in io.seqware.webservice.controller

CustomIusFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomIusFacadeREST

CustomIusLinkFacadeREST - Class in io.seqware.webservice.controller

CustomIusLinkFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomIusLinkFacadeREST

CustomIusWorkflowRunsFacadeREST - Class in io.seqware.webservice.controller

CustomIusWorkflowRunsFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomIusWorkflowRunsFacadeREST

CustomLaneAttributeFacadeREST - Class in io.seqware.webservice.controller

CustomLaneAttributeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomLaneAttributeFacadeREST

CustomLaneFacadeREST - Class in io.seqware.webservice.controller

CustomLaneFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomLaneFacadeREST

CustomLaneLinkFacadeREST - Class in io.seqware.webservice.controller

CustomLaneLinkFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomLaneLinkFacadeREST

CustomLaneTypeFacadeREST - Class in io.seqware.webservice.controller

CustomLaneTypeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomLaneTypeFacadeREST

CustomLaneWorkflowRunsFacadeREST - Class in io.seqware.webservice.controller

CustomLaneWorkflowRunsFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomLaneWorkflowRunsFacadeREST

CustomLibrarySelectionFacadeREST - Class in io.seqware.webservice.controller

CustomLibrarySelectionFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomLibrarySelectionFacadeREST

CustomLibrarySourceFacadeREST - Class in io.seqware.webservice.controller

CustomLibrarySourceFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomLibrarySourceFacadeREST

CustomLibraryStrategyFacadeREST - Class in io.seqware.webservice.controller

CustomLibraryStrategyFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomLibraryStrategyFacadeREST

CustomOrganismFacadeREST - Class in io.seqware.webservice.controller

CustomOrganismFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomOrganismFacadeREST

CustomPlatformFacadeREST - Class in io.seqware.webservice.controller

CustomPlatformFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomPlatformFacadeREST

CustomProcessingAttributeFacadeREST - Class in io.seqware.webservice.controller

CustomProcessingAttributeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomProcessingAttributeFacadeREST

CustomProcessingExperimentsFacadeREST - Class in io.seqware.webservice.controller

CustomProcessingExperimentsFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomProcessingExperimentsFacadeREST

CustomProcessingFacadeREST - Class in io.seqware.webservice.controller

CustomProcessingFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomProcessingFacadeREST

CustomProcessingFilesFacadeREST - Class in io.seqware.webservice.controller

CustomProcessingFilesFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomProcessingFilesFacadeREST

CustomProcessingIusFacadeREST - Class in io.seqware.webservice.controller

CustomProcessingIusFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomProcessingIusFacadeREST

CustomProcessingLanesFacadeREST - Class in io.seqware.webservice.controller

CustomProcessingLanesFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomProcessingLanesFacadeREST

CustomProcessingRelationshipFacadeREST - Class in io.seqware.webservice.controller

CustomProcessingRelationshipFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomProcessingRelationshipFacadeREST

CustomProcessingSamplesFacadeREST - Class in io.seqware.webservice.controller

CustomProcessingSamplesFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomProcessingSamplesFacadeREST

CustomProcessingSequencerRunsFacadeREST - Class in io.seqware.webservice.controller

CustomProcessingSequencerRunsFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomProcessingSequencerRunsFacadeREST

CustomProcessingStudiesFacadeREST - Class in io.seqware.webservice.controller

CustomProcessingStudiesFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomProcessingStudiesFacadeREST

CustomRegistrationFacadeREST - Class in io.seqware.webservice.controller

CustomRegistrationFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomRegistrationFacadeREST

CustomSampleAttributeFacadeREST - Class in io.seqware.webservice.controller

CustomSampleAttributeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomSampleAttributeFacadeREST

CustomSampleFacadeREST - Class in io.seqware.webservice.controller

CustomSampleFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomSampleFacadeREST

CustomSampleLinkFacadeREST - Class in io.seqware.webservice.controller

CustomSampleLinkFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomSampleLinkFacadeREST

CustomSampleRelationshipFacadeREST - Class in io.seqware.webservice.controller

CustomSampleRelationshipFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomSampleRelationshipFacadeREST

CustomSampleReportFacadeREST - Class in io.seqware.webservice.controller

CustomSampleReportFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomSampleReportFacadeREST

CustomSampleSearchAttributeFacadeREST - Class in io.seqware.webservice.controller

CustomSampleSearchAttributeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomSampleSearchAttributeFacadeREST

CustomSampleSearchFacadeREST - Class in io.seqware.webservice.controller

CustomSampleSearchFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomSampleSearchFacadeREST

CustomSequencerRunAttributeFacadeREST - Class in io.seqware.webservice.controller

CustomSequencerRunAttributeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomSequencerRunAttributeFacadeREST

CustomSequencerRunFacadeREST - Class in io.seqware.webservice.controller

CustomSequencerRunFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomSequencerRunFacadeREST

CustomShareExperimentFacadeREST - Class in io.seqware.webservice.controller

CustomShareExperimentFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomShareExperimentFacadeREST

CustomShareFileFacadeREST - Class in io.seqware.webservice.controller

CustomShareFileFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomShareFileFacadeREST

CustomShareLaneFacadeREST - Class in io.seqware.webservice.controller

CustomShareLaneFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomShareLaneFacadeREST

CustomShareProcessingFacadeREST - Class in io.seqware.webservice.controller

CustomShareProcessingFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomShareProcessingFacadeREST

CustomShareSampleFacadeREST - Class in io.seqware.webservice.controller

CustomShareSampleFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomShareSampleFacadeREST

CustomShareStudyFacadeREST - Class in io.seqware.webservice.controller

CustomShareStudyFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomShareStudyFacadeREST

CustomShareWorkflowRunFacadeREST - Class in io.seqware.webservice.controller

CustomShareWorkflowRunFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomShareWorkflowRunFacadeREST

CustomStudyAttributeFacadeREST - Class in io.seqware.webservice.controller

CustomStudyAttributeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomStudyAttributeFacadeREST

CustomStudyFacadeREST - Class in io.seqware.webservice.controller

CustomStudyFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomStudyFacadeREST

CustomStudyLinkFacadeREST - Class in io.seqware.webservice.controller

CustomStudyLinkFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomStudyLinkFacadeREST

CustomStudyTypeFacadeREST - Class in io.seqware.webservice.controller

CustomStudyTypeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomStudyTypeFacadeREST

CustomWorkflowAttributeFacadeREST - Class in io.seqware.webservice.controller

CustomWorkflowAttributeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomWorkflowAttributeFacadeREST

CustomWorkflowFacadeREST - Class in io.seqware.webservice.controller

CustomWorkflowFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomWorkflowFacadeREST

CustomWorkflowParamFacadeREST - Class in io.seqware.webservice.controller

CustomWorkflowParamFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomWorkflowParamFacadeREST

CustomWorkflowParamValueFacadeREST - Class in io.seqware.webservice.controller

CustomWorkflowParamValueFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomWorkflowParamValueFacadeREST

CustomWorkflowRunAttributeFacadeREST - Class in io.seqware.webservice.controller

CustomWorkflowRunAttributeFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomWorkflowRunAttributeFacadeREST

CustomWorkflowRunFacadeREST - Class in io.seqware.webservice.controller

CustomWorkflowRunFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomWorkflowRunFacadeREST

CustomWorkflowRunParamFacadeREST - Class in io.seqware.webservice.controller

CustomWorkflowRunParamFacadeREST() - Constructor for class io.seqware.webservice.controller.CustomWorkflowRunParamFacadeREST

CycleChecker - Class in net.sourceforge.seqware.pipeline.plugins

CycleChecker class.

CycleChecker() - Constructor for class net.sourceforge.seqware.pipeline.plugins.CycleChecker

Constructor for CycleChecker.

CycleCheckResource - Class in net.sourceforge.seqware.webservice.resources.queries

CycleCheckResource class.

CycleCheckResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.CycleCheckResource

Constructor for CycleCheckResource.

D

DatabaseIDResource - Class in net.sourceforge.seqware.webservice.resources.tables

DatabaseIDResource class.

DatabaseIDResource(String) - Constructor for class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource

Constructor for DatabaseIDResource.

DatabaseResource - Class in net.sourceforge.seqware.webservice.resources.tables

DatabaseResource class.

DatabaseResource(String) - Constructor for class net.sourceforge.seqware.webservice.resources.tables.DatabaseResource

Constructor for DatabaseResource.

dataDecryptionKey - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

dataEncryptionKey - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

dataEncryptionKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

DateFormatterAdapter - Class in io.seqware.webservice.adapter

A JAXB Adapter to convert Date to ISO8601 date time strings when generating XML and JSON.

DateFormatterAdapter() - Constructor for class io.seqware.webservice.adapter.DateFormatterAdapter

Daxgenerator - Class in net.sourceforge.seqware.pipeline.daxgenerator

Daxgenerator class.

Daxgenerator() - Constructor for class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator

DaxgeneratorV2 - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus

DaxgeneratorV2() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.DaxgeneratorV2

DB_Check - Class in io.seqware.pipeline.plugins.sanity.checks

Checks that the database you're pointing to (if there is one) is consistent with the web service you're pointing to

DB_Check() - Constructor for class io.seqware.pipeline.plugins.sanity.checks.DB_Check

DB_CONN_STRING - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys

DB_NAME - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys

DB_PASS - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys

DB_SERVER - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys

DB_USER - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys

DB_WS_ConsistencyCheck - Class in io.seqware.pipeline.plugins.sanity.checks

Checks that the database you're pointing to (if there is one) is consistent with the web service you're pointing to

DB_WS_ConsistencyCheck() - Constructor for class io.seqware.pipeline.plugins.sanity.checks.DB_WS_ConsistencyCheck

DBAccess - Class in net.sourceforge.seqware.common.factory

DBAccess class.

DBCOULDNOTDISCONNECT - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant DBCOULDNOTDISCONNECT=81

DBCOULDNOTINITIALIZE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant DBCOULDNOTINITIALIZE=80

DEBUG - Static variable in class io.seqware.cli.Main

debug(Object) - Static method in class net.sourceforge.seqware.common.util.Log

See Category.debug(Object).

debug(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log

See Category.debug(Object,Throwable).

Debug - Class in net.sourceforge.solexatools

Debug class.

Debug() - Constructor for class net.sourceforge.solexatools.Debug

DeciderInterface - Interface in net.sourceforge.seqware.pipeline.decider

DeciderInterface interface.

DEFAULT_ENGINE - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

DEFAULT_QUEUE_LENGTH - Static variable in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

defaults - Variable in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

delete(Experiment, boolean) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

delete.

delete(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService

delete.

delete(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService

delete.

delete(File, boolean) - Method in interface net.sourceforge.seqware.common.business.FileService

delete.

delete(Experiment, boolean) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

delete.

delete(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl

delete.

delete(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl

delete.

delete(File, boolean) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

delete.

delete(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl

delete.

delete(IUS, boolean) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

delete.

delete(Lane, boolean) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

delete.

delete(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl

delete.

delete(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl

delete.

delete(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl

delete.

delete(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl

delete.

delete(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl

delete.

delete(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl

delete.

delete(Processing, boolean) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

delete.

delete(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl

delete.

delete(Sample, boolean) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

delete.

delete(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

delete.

delete(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl

delete.

delete(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl

delete.

delete(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl

delete.

delete(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl

delete.

delete(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl

delete.

delete(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl

delete.

delete(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl

delete.

delete(Study, boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

delete.

delete(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl

delete.

delete(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl

delete.

delete(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl

delete.

delete(WorkflowRun, boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

delete.

delete(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

delete.

delete(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService

delete.

delete(IUS, boolean) - Method in interface net.sourceforge.seqware.common.business.IUSService

delete.

delete(Lane, boolean) - Method in interface net.sourceforge.seqware.common.business.LaneService

delete.

delete(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService

delete.

delete(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService

delete.

delete(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService

delete.

delete(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService

delete.

delete(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService

delete.

delete(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService

delete.

delete(Processing, boolean) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

delete.

delete(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService

delete.

delete(Sample, boolean) - Method in interface net.sourceforge.seqware.common.business.SampleService

delete.

delete(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

delete.

delete(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService

delete.

delete(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService

delete.

delete(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService

delete.

delete(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService

delete.

delete(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService

delete.

delete(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService

delete.

delete(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService

delete.

delete(Study, boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService

delete.

delete(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService

delete.

delete(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService

delete.

delete(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService

delete.

delete(WorkflowRun, boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

delete.

delete(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

delete.

delete(ExperimentAttribute) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO

delete.

delete(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

delete.

delete(ExperimentLink) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO

delete.

delete(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO

delete.

delete(FileAttribute) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO

delete.

delete(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

delete.

delete(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate

delete.

delete(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

delete.

delete(ExperimentLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate

delete.

delete(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate

delete.

delete(FileAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate

delete.

delete(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

delete.

delete(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate

delete.

delete(IUSAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate

delete.

delete(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

delete.

delete(IUSLink) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO

delete.

delete(IUSLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate

delete.

delete(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO

delete.

delete(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate

delete.

delete(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

delete.

delete(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

delete.

delete(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO

delete.

delete(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate

delete.

delete(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate

delete.

delete(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

delete.

delete(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate

delete.

delete(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate

delete.

delete(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate

delete.

delete(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate

delete.

delete(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate

delete.

delete(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate

delete.

delete(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate

delete.

delete(SampleAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate

delete.

delete(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

delete.

delete(SampleLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate

delete.

delete(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

delete.

delete(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate

delete.

delete(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate

delete.

delete(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate

delete.

delete(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate

delete.

delete(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate

delete.

delete(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate

delete.

delete(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate

delete.

delete(StudyAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate

delete.

delete(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

delete.

delete(StudyLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate

delete.

delete(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate

delete.

delete(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

delete.

delete(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate

delete.

delete(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate

delete.

delete(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate

delete.

delete(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

delete.

delete(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate

delete.

delete(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO

delete.

delete(IUSAttribute) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO

delete.

delete(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

delete.

delete(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

delete.

delete(SortedSet<Lane>) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

delete.

delete(ProcessingAttribute) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO

delete.

delete(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

delete.

delete(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO

delete.

delete(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO

delete.

delete(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO

delete.

delete(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO

delete.

delete(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO

delete.

delete(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO

delete.

delete(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO

delete.

delete(SampleAttribute) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO

delete.

delete(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

delete.

delete(SampleLink) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO

delete.

delete(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

delete.

delete(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO

delete.

delete(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO

delete.

delete(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO

delete.

delete(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO

delete.

delete(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO

delete.

delete(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO

delete.

delete(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO

delete.

delete(StudyAttribute) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO

delete.

delete(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

delete.

delete(StudyLink) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO

delete.

delete(WorkflowAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO

delete.

delete(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

delete.

delete(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO

delete.

delete(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO

delete.

delete(WorkflowRunAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO

delete.

delete(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

delete.

delete(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO

delete.

delete() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter

delete() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource

delete() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource

deleteAll(List<File>, boolean) - Method in interface net.sourceforge.seqware.common.business.FileService

deleteAll.

deleteAll(List<File>, boolean) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

deleteAll.

deleteAll(List<File>) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

deleteAll.

deleteAll(List<File>) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

deleteAll.

deleteAllWithFolderStore(List<File>) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

deleteAllWithFolderStore.

deleteAllWithFolderStore(List<File>) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

deleteAllWithFolderStore.

deleteAttribute() - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource

deleteAttribute.

deleteAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource

deleteAttribute.

deleteDirectoryRecursive(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

deleteDirectoryRecursive.

DeleteLoadedIndexPageController - Class in net.sourceforge.solexatools.webapp.controller

DeleteLoadedIndexPageController class.

DeleteLoadedIndexPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController

Constructor for DeleteLoadedIndexPageController.

deleteRecursive(Integer, Set<ModelAccessionIDTuple>, String) - Method in class io.seqware.webservice.controller.CustomWorkflowRunFacadeREST

The actual delete method, container managed JTA transactions should handle rollback and atomic operations

DeleteTempFile(Registration) - Method in class net.sourceforge.solexatools.webapp.controller.LoginController

DeleteTempFile.

DeletionDB - Class in net.sourceforge.seqware.pipeline.plugins.deletion

A workflow run deletion tool for your SeqWare metadb

DeletionDB() - Constructor for class net.sourceforge.seqware.pipeline.plugins.deletion.DeletionDB

Constructor for HelloWorld.

desc - Variable in enum net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility.HumanProvenanceFilters

describeInterfaceAndImplementation(Object, String) - Static method in class net.sourceforge.solexatools.Debug

describeInterfaceAndImplementation.

description - Variable in class net.sourceforge.seqware.common.module.ReturnValue

determineRelativeBundlePath(OptionSet) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility

Determine the bundle path from the provided options

determineStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

Map a normal status to whether a workflow run completed, failed, or other (submitted, pending, etc.) (the states that we care about for the decider)

difference(Set<T>, Set<T>) - Static method in class net.sourceforge.seqware.pipeline.tools.SetOperations

DIRECT_SEARCH - Static variable in class net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource

A direct search uses the workflow_run_input_files table rather than attempting a search via the ius_workflow_run and lane_workflow_run and processing hierarchy

DIRECTORYNOTREADABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant DIRECTORYNOTREADABLE=3

DIRECTORYNOTWRITABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant DIRECTORYNOTWRITABLE=11

directRetrieveWorkflowRuns(List<Integer>, List<Integer>) - Static method in class net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource

Use SQL to directly retrieve relevant workflows runs (defined as any workflow runs that include one or more files in the set we were given)

dirPathExistsAndReadable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

dirPathExistsAndReadable.

dirPathExistsAndWritable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

dirPathExistsAndWritable.

do_run() - Method in class io.seqware.pipeline.plugins.sanity.SanityCheck

Performs the main tasks for the plugin.

do_run() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

do_run() - Method in class net.sourceforge.seqware.pipeline.module.Module

do_run.

do_run() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface

Performs the main tasks for the module.

do_run() - Method in class net.sourceforge.seqware.pipeline.module.TestModule

do_run.

do_run() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

do_run.

do_run() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver

Deprecated.

do_run.

do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle

do_run.

do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

do_run.

do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

do_run.

do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

do_run.

do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

do_run.

do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory

do_run() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.deletion.DeletionDB

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.fileprovenance.FileProvenanceReporter

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter

Performs the main tasks for the plugin.

do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker

Performs the main tasks for the plugin.

do_summary() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface

Just returns a summary of what would be run.

do_summary() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

do_test() - Method in class io.seqware.pipeline.plugins.sanity.SanityCheck

Perform any active system testing here.

do_test() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

do_test() - Method in class net.sourceforge.seqware.pipeline.module.Module

do_test.

do_test() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.module.TestModule

do_test.

do_test() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

do_test.

do_test() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver

Deprecated.

do_test.

do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle

do_test.

do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

do_test.

do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

do_test.

do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

do_test.

do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

do_test.

do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory

Things to check: * FIXME

do_test() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.deletion.DeletionDB

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.fileprovenance.FileProvenanceReporter

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter

Perform any active system testing here.

do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker

Perform any active system testing here.

do_verify_input() - Method in class net.sourceforge.seqware.pipeline.module.Module

do_verify_input.

do_verify_input() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface

Input data validation code goes here.

do_verify_input() - Method in class net.sourceforge.seqware.pipeline.module.TestModule

do_verify_input.

do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

do_verify_input.

do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver

Deprecated.

do_verify_input.

do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle

do_verify_input.

do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

do_verify_input.

do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

do_verify_input.

do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

do_verify_input.

do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

do_verify_input.

do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory

do_verify_output() - Method in class net.sourceforge.seqware.pipeline.module.Module

do_verify_output.

do_verify_output() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface

Perform post-task tests here.

do_verify_output() - Method in class net.sourceforge.seqware.pipeline.module.TestModule

do_verify_output.

do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

do_verify_output.

do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver

Deprecated.

do_verify_output.

do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle

do_verify_output.

do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

do_verify_output.

do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

do_verify_output.

do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

do_verify_output.

do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

do_verify_output.

do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory

do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.module.Module

do_verify_parameters.

do_verify_parameters() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface

Parameter validation code goes here.

do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.module.TestModule

do_verify_parameters.

do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

do_verify_parameters.

do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver

Deprecated.

do_verify_parameters.

do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle

do_verify_parameters.

do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

do_verify_parameters.

do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

do_verify_parameters.

do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

do_verify_parameters.

do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

do_verify_parameters.

do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory

doCreateTableJson(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

doCreateTableJson.

doFinalCheck(String, String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

allow to user to do the final check and decide to run or cancel the decider e.g.

doInit() - Method in class net.sourceforge.seqware.webservice.resources.BasicResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter

doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter

doInit() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentLibraryDesignResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentSpotDesignReadSpecResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentSpotDesignResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileLinkReportResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileReverseHierarchyDisplayResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusFilesServerResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusSearchServerResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrariesResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySelectionResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySourceResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryStrategyResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.OrganismResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.PlatformResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.RootSampleResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource

doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyTypeResource

doOldRun() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

This is the original run method from the old Workflow launcher.

doRetrieveListElements(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

doRetrieveListElements.

doSetupReport(HttpServletRequest) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController

doSetupReport.

DownloaderController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController

DownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.DownloaderController

Constructor for DownloaderController.

DownloadFileListController - Class in net.sourceforge.solexatools.webapp.controller

DownloadFileListController class.

DownloadFileListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Constructor for DownloadFileListController.

dropDatabase() - Static method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreatorWrapper

dropDatabase.

dropDatabase() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

dropDatabase.

dropDatabaseWithUsers() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

Drop a database schema even when users are connected to it

Dtos - Class in net.sourceforge.seqware.webservice.dto

Methods to convert between domain objects and dtos.

Dtos() - Constructor for class net.sourceforge.seqware.webservice.dto.Dtos

E

edit(T) - Method in class io.seqware.webservice.generated.controller.AbstractFacade

edit(ExpenseAttribute) - Method in class io.seqware.webservice.generated.controller.ExpenseAttributeFacadeREST

edit(Expense) - Method in class io.seqware.webservice.generated.controller.ExpenseFacadeREST

edit(ExperimentAttribute) - Method in class io.seqware.webservice.generated.controller.ExperimentAttributeFacadeREST

edit(Experiment) - Method in class io.seqware.webservice.generated.controller.ExperimentFacadeREST

edit(ExperimentLibraryDesign) - Method in class io.seqware.webservice.generated.controller.ExperimentLibraryDesignFacadeREST

edit(ExperimentLink) - Method in class io.seqware.webservice.generated.controller.ExperimentLinkFacadeREST

edit(ExperimentSpotDesign) - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignFacadeREST

edit(ExperimentSpotDesignReadSpec) - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignReadSpecFacadeREST

edit(FileAttribute) - Method in class io.seqware.webservice.generated.controller.FileAttributeFacadeREST

edit(File) - Method in class io.seqware.webservice.generated.controller.FileFacadeREST

edit(FileReport) - Method in class io.seqware.webservice.generated.controller.FileReportFacadeREST

edit(FileType) - Method in class io.seqware.webservice.generated.controller.FileTypeFacadeREST

edit(InvoiceAttribute) - Method in class io.seqware.webservice.generated.controller.InvoiceAttributeFacadeREST

edit(Invoice) - Method in class io.seqware.webservice.generated.controller.InvoiceFacadeREST

edit(IusAttribute) - Method in class io.seqware.webservice.generated.controller.IusAttributeFacadeREST

edit(Ius) - Method in class io.seqware.webservice.generated.controller.IusFacadeREST

edit(IusLink) - Method in class io.seqware.webservice.generated.controller.IusLinkFacadeREST

edit(IusWorkflowRuns) - Method in class io.seqware.webservice.generated.controller.IusWorkflowRunsFacadeREST

edit(LaneAttribute) - Method in class io.seqware.webservice.generated.controller.LaneAttributeFacadeREST

edit(Lane) - Method in class io.seqware.webservice.generated.controller.LaneFacadeREST

edit(LaneLink) - Method in class io.seqware.webservice.generated.controller.LaneLinkFacadeREST

edit(LaneType) - Method in class io.seqware.webservice.generated.controller.LaneTypeFacadeREST

edit(LaneWorkflowRuns) - Method in class io.seqware.webservice.generated.controller.LaneWorkflowRunsFacadeREST

edit(LibrarySelection) - Method in class io.seqware.webservice.generated.controller.LibrarySelectionFacadeREST

edit(LibrarySource) - Method in class io.seqware.webservice.generated.controller.LibrarySourceFacadeREST

edit(LibraryStrategy) - Method in class io.seqware.webservice.generated.controller.LibraryStrategyFacadeREST

edit(Organism) - Method in class io.seqware.webservice.generated.controller.OrganismFacadeREST

edit(Platform) - Method in class io.seqware.webservice.generated.controller.PlatformFacadeREST

edit(ProcessingAttribute) - Method in class io.seqware.webservice.generated.controller.ProcessingAttributeFacadeREST

edit(ProcessingExperiments) - Method in class io.seqware.webservice.generated.controller.ProcessingExperimentsFacadeREST

edit(Processing) - Method in class io.seqware.webservice.generated.controller.ProcessingFacadeREST

edit(ProcessingFiles) - Method in class io.seqware.webservice.generated.controller.ProcessingFilesFacadeREST

edit(ProcessingIus) - Method in class io.seqware.webservice.generated.controller.ProcessingIusFacadeREST

edit(ProcessingLanes) - Method in class io.seqware.webservice.generated.controller.ProcessingLanesFacadeREST

edit(ProcessingRelationship) - Method in class io.seqware.webservice.generated.controller.ProcessingRelationshipFacadeREST

edit(ProcessingSamples) - Method in class io.seqware.webservice.generated.controller.ProcessingSamplesFacadeREST

edit(ProcessingSequencerRuns) - Method in class io.seqware.webservice.generated.controller.ProcessingSequencerRunsFacadeREST

edit(ProcessingStudies) - Method in class io.seqware.webservice.generated.controller.ProcessingStudiesFacadeREST

edit(Registration) - Method in class io.seqware.webservice.generated.controller.RegistrationFacadeREST

edit(SampleAttribute) - Method in class io.seqware.webservice.generated.controller.SampleAttributeFacadeREST

edit(Sample) - Method in class io.seqware.webservice.generated.controller.SampleFacadeREST

edit(SampleLink) - Method in class io.seqware.webservice.generated.controller.SampleLinkFacadeREST

edit(SampleRelationship) - Method in class io.seqware.webservice.generated.controller.SampleRelationshipFacadeREST

edit(SampleReport) - Method in class io.seqware.webservice.generated.controller.SampleReportFacadeREST

edit(SampleSearchAttribute) - Method in class io.seqware.webservice.generated.controller.SampleSearchAttributeFacadeREST

edit(SampleSearch) - Method in class io.seqware.webservice.generated.controller.SampleSearchFacadeREST

edit(SequencerRunAttribute) - Method in class io.seqware.webservice.generated.controller.SequencerRunAttributeFacadeREST

edit(SequencerRun) - Method in class io.seqware.webservice.generated.controller.SequencerRunFacadeREST

edit(ShareExperiment) - Method in class io.seqware.webservice.generated.controller.ShareExperimentFacadeREST

edit(ShareFile) - Method in class io.seqware.webservice.generated.controller.ShareFileFacadeREST

edit(ShareLane) - Method in class io.seqware.webservice.generated.controller.ShareLaneFacadeREST

edit(ShareProcessing) - Method in class io.seqware.webservice.generated.controller.ShareProcessingFacadeREST

edit(ShareSample) - Method in class io.seqware.webservice.generated.controller.ShareSampleFacadeREST

edit(ShareStudy) - Method in class io.seqware.webservice.generated.controller.ShareStudyFacadeREST

edit(ShareWorkflowRun) - Method in class io.seqware.webservice.generated.controller.ShareWorkflowRunFacadeREST

edit(StudyAttribute) - Method in class io.seqware.webservice.generated.controller.StudyAttributeFacadeREST

edit(Study) - Method in class io.seqware.webservice.generated.controller.StudyFacadeREST

edit(StudyLink) - Method in class io.seqware.webservice.generated.controller.StudyLinkFacadeREST

edit(StudyType) - Method in class io.seqware.webservice.generated.controller.StudyTypeFacadeREST

edit(WorkflowAttribute) - Method in class io.seqware.webservice.generated.controller.WorkflowAttributeFacadeREST

edit(Workflow) - Method in class io.seqware.webservice.generated.controller.WorkflowFacadeREST

edit(WorkflowParam) - Method in class io.seqware.webservice.generated.controller.WorkflowParamFacadeREST

edit(WorkflowParamValue) - Method in class io.seqware.webservice.generated.controller.WorkflowParamValueFacadeREST

edit(WorkflowRunAttribute) - Method in class io.seqware.webservice.generated.controller.WorkflowRunAttributeFacadeREST

edit(WorkflowRun) - Method in class io.seqware.webservice.generated.controller.WorkflowRunFacadeREST

edit(WorkflowRunParam) - Method in class io.seqware.webservice.generated.controller.WorkflowRunParamFacadeREST

edit_JSON(Object) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

edit_XML(Object) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

emitOptionsFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

Engines - Class in io.seqware

Engines() - Constructor for class io.seqware.Engines

ENGINES - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

ENGINES_LIST - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

ensureSafe(String) - Static method in class net.sourceforge.seqware.common.util.Str

Throws an exception if the string does not match [a-zA-Z0-9_-]+, otherwise a no-op.

EntityController - Class in net.sourceforge.solexatools.webapp.controller

The controller.

EntityController() - Constructor for class net.sourceforge.solexatools.webapp.controller.EntityController

Constructor for EntityController.

Environment - Class in net.sourceforge.seqware.pipeline.workflowV2.model

Environment() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

EnvUtil - Class in net.sourceforge.seqware.queryengine.webservice.util

EnvUtil class.

EnvUtil() - Constructor for class net.sourceforge.seqware.queryengine.webservice.util.EnvUtil

ENVVARNOTFOUND - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant ENVVARNOTFOUND=14

equals(Object) - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple

equals(Object) - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple

equals(Object) - Method in class io.seqware.webservice.generated.model.Expense

equals(Object) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute

equals(Object) - Method in class io.seqware.webservice.generated.model.Experiment

equals(Object) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute

equals(Object) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

equals(Object) - Method in class io.seqware.webservice.generated.model.ExperimentLink

equals(Object) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

equals(Object) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

equals(Object) - Method in class io.seqware.webservice.generated.model.File

equals(Object) - Method in class io.seqware.webservice.generated.model.FileAttribute

equals(Object) - Method in class io.seqware.webservice.generated.model.FileReport

equals(Object) - Method in class io.seqware.webservice.generated.model.FileType

equals(Object) - Method in class io.seqware.webservice.generated.model.Invoice

equals(Object) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute

equals(Object) - Method in class io.seqware.webservice.generated.model.Ius

equals(Object) - Method in class io.seqware.webservice.generated.model.IusAttribute

equals(Object) - Method in class io.seqware.webservice.generated.model.IusLink

equals(Object) - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns

equals(Object) - Method in class io.seqware.webservice.generated.model.Lane

equals(Object) - Method in class io.seqware.webservice.generated.model.LaneAttribute

equals(Object) - Method in class io.seqware.webservice.generated.model.LaneLink

equals(Object) - Method in class io.seqware.webservice.generated.model.LaneType

equals(Object) - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns

equals(Object) - Method in class io.seqware.webservice.generated.model.LibrarySelection

equals(Object) - Method in class io.seqware.webservice.generated.model.LibrarySource

equals(Object) - Method in class io.seqware.webservice.generated.model.LibraryStrategy

equals(Object) - Method in class io.seqware.webservice.generated.model.Organism

equals(Object) - Method in class io.seqware.webservice.generated.model.Platform

equals(Object) - Method in class io.seqware.webservice.generated.model.Processing

equals(Object) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute

equals(Object) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

equals(Object) - Method in class io.seqware.webservice.generated.model.ProcessingFiles

equals(Object) - Method in class io.seqware.webservice.generated.model.ProcessingIus

equals(Object) - Method in class io.seqware.webservice.generated.model.ProcessingLanes

equals(Object) - Method in class io.seqware.webservice.generated.model.ProcessingRelationship

equals(Object) - Method in class io.seqware.webservice.generated.model.ProcessingSamples

equals(Object) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

equals(Object) - Method in class io.seqware.webservice.generated.model.ProcessingStudies

equals(Object) - Method in class io.seqware.webservice.generated.model.Registration

equals(Object) - Method in class io.seqware.webservice.generated.model.Sample

equals(Object) - Method in class io.seqware.webservice.generated.model.SampleAttribute

equals(Object) - Method in class io.seqware.webservice.generated.model.SampleLink

equals(Object) - Method in class io.seqware.webservice.generated.model.SampleRelationship

equals(Object) - Method in class io.seqware.webservice.generated.model.SampleReport

equals(Object) - Method in class io.seqware.webservice.generated.model.SampleSearch

equals(Object) - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute

equals(Object) - Method in class io.seqware.webservice.generated.model.SequencerRun

equals(Object) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute

equals(Object) - Method in class io.seqware.webservice.generated.model.ShareExperiment

equals(Object) - Method in class io.seqware.webservice.generated.model.ShareFile

equals(Object) - Method in class io.seqware.webservice.generated.model.ShareLane

equals(Object) - Method in class io.seqware.webservice.generated.model.ShareProcessing

equals(Object) - Method in class io.seqware.webservice.generated.model.ShareSample

equals(Object) - Method in class io.seqware.webservice.generated.model.ShareStudy

equals(Object) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

equals(Object) - Method in class io.seqware.webservice.generated.model.Study

equals(Object) - Method in class io.seqware.webservice.generated.model.StudyAttribute

equals(Object) - Method in class io.seqware.webservice.generated.model.StudyLink

equals(Object) - Method in class io.seqware.webservice.generated.model.StudyType

equals(Object) - Method in class io.seqware.webservice.generated.model.Workflow

equals(Object) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute

equals(Object) - Method in class io.seqware.webservice.generated.model.WorkflowParam

equals(Object) - Method in class io.seqware.webservice.generated.model.WorkflowParamValue

equals(Object) - Method in class io.seqware.webservice.generated.model.WorkflowRun

equals(Object) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute

equals(Object) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

equals(Object) - Method in class net.sourceforge.seqware.common.model.Expense

equals(Object) - Method in class net.sourceforge.seqware.common.model.Experiment

equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

equals(Object) - Method in class net.sourceforge.seqware.common.model.File

equals(Object) - Method in class net.sourceforge.seqware.common.model.FileType

equals(Object) - Method in class net.sourceforge.seqware.common.model.Invoice

equals(Object) - Method in class net.sourceforge.seqware.common.model.IUS

equals(Object) - Method in class net.sourceforge.seqware.common.model.Lane

equals(Object) - Method in class net.sourceforge.seqware.common.model.LibrarySelection

equals(Object) - Method in class net.sourceforge.seqware.common.model.LibrarySource

equals(Object) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy

equals(Object) - Method in class net.sourceforge.seqware.common.model.Organism

equals(Object) - Method in class net.sourceforge.seqware.common.model.Platform

equals(Object) - Method in class net.sourceforge.seqware.common.model.Processing

equals(Object) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

equals(Object) - Method in class net.sourceforge.seqware.common.model.Registration

equals(Object) - Method in class net.sourceforge.seqware.common.model.Sample

equals(Object) - Method in class net.sourceforge.seqware.common.model.SampleAttribute

equals(Object) - Method in class net.sourceforge.seqware.common.model.SequencerRun

equals(Object) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

equals(Object) - Method in class net.sourceforge.seqware.common.model.ShareStudy

equals(Object) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

equals(Object) - Method in class net.sourceforge.seqware.common.model.Study

equals(Object) - Method in class net.sourceforge.seqware.common.model.StudyAttribute

equals(Object) - Method in class net.sourceforge.seqware.common.model.StudyType

equals(Object) - Method in class net.sourceforge.seqware.common.model.Workflow

equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

equals(Object) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument

equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

error(Object) - Static method in class net.sourceforge.seqware.common.util.Log

See Category.error(Object).

error(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log

See Category.error(Object,Throwable).

evaluateReturn(Module, String) - Method in class net.sourceforge.seqware.pipeline.runner.Runner

evaluateReturn.

evict(Object) - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions

evict.

ExceptionTools - Class in net.sourceforge.seqware.common.util.exceptiontools

ExceptionTools class.

ExceptionTools() - Constructor for class net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools

executeQuery(String, ResultSetHandler<T>) - Method in class io.seqware.pipeline.plugins.sanity.QueryRunner

executeQuery(String, ResultSetHandler<T>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

executeQuery.

executeQuery(String, ResultSetHandler<T>) - Method in class net.sourceforge.seqware.pipeline.plugins.checkdb.SelectQueryRunner

executeUpdate(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

executeUpdate.

existsExperiment(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel

existsFile(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel

existsIUS(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel

existsLane(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel

existsObject(String, String, JaxbObject, Object) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel

existsProcessing(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel

existsSample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel

existsSequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel

existsStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel

existsWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel

existsWorkflowRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel

ExitException - Exception in net.sourceforge.seqware.common.util

Created by IntelliJ IDEA.

ExitException(int) - Constructor for exception net.sourceforge.seqware.common.util.ExitException

Constructor for ExitException.

exitStatus - Variable in class net.sourceforge.seqware.common.module.ReturnValue

expandVariables(Map<String, String>) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools

expandVariables(Map<String, String>, Map<String, String>) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools

expandVariables(Map<String, String>, Map<String, String>, boolean) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools

expansion(String) - Static method in class net.sourceforge.seqware.common.util.TabExpansionUtil

Produce output resembling Postgres with one "table" per record

Expense - Class in io.seqware.webservice.generated.model

Expense() - Constructor for class io.seqware.webservice.generated.model.Expense

Expense(Integer) - Constructor for class io.seqware.webservice.generated.model.Expense

Expense - Class in net.sourceforge.seqware.common.model

Expense class.

Expense() - Constructor for class net.sourceforge.seqware.common.model.Expense

Constructor for Expense.

ExpenseAttribute - Class in io.seqware.webservice.generated.model

ExpenseAttribute() - Constructor for class io.seqware.webservice.generated.model.ExpenseAttribute

ExpenseAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.ExpenseAttribute

ExpenseAttributeFacadeREST - Class in io.seqware.webservice.generated.controller

ExpenseAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ExpenseAttributeFacadeREST

ExpenseFacadeREST - Class in io.seqware.webservice.generated.controller

ExpenseFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ExpenseFacadeREST

Experiment - Class in io.seqware.webservice.generated.model

Experiment() - Constructor for class io.seqware.webservice.generated.model.Experiment

Experiment(Integer) - Constructor for class io.seqware.webservice.generated.model.Experiment

Experiment(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.Experiment

Experiment - Class in net.sourceforge.seqware.common.model

Experiment() - Constructor for class net.sourceforge.seqware.common.model.Experiment

Constructor for Experiment.

EXPERIMENT_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant EXPERIMENT_ATTRIBUTES="Header.EXPERIMENT_ATTRIBUTES.getTitle()"

EXPERIMENT_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant EXPERIMENT_NAME="Header.EXPERIMENT_NAME.getTitle()"

EXPERIMENT_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant

Constant EXPERIMENT_PREFIX="exp_"

EXPERIMENT_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant EXPERIMENT_SWA="Header.EXPERIMENT_SWA.getTitle()"

EXPERIMENT_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant EXPERIMENT_TAG_PREFIX="Header.EXPERIMENT_TAG_PREFIX.getTitle()"

ExperimentAttribute - Class in io.seqware.webservice.generated.model

ExperimentAttribute() - Constructor for class io.seqware.webservice.generated.model.ExperimentAttribute

ExperimentAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.ExperimentAttribute

ExperimentAttribute - Class in net.sourceforge.seqware.common.model

ExperimentAttribute generated by hbm2java

ExperimentAttribute() - Constructor for class net.sourceforge.seqware.common.model.ExperimentAttribute

Constructor for ExperimentAttribute.

ExperimentAttribute(int, Experiment) - Constructor for class net.sourceforge.seqware.common.model.ExperimentAttribute

Constructor for ExperimentAttribute.

ExperimentAttribute(int, Experiment, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.ExperimentAttribute

Constructor for ExperimentAttribute.

ExperimentAttributeDAO - Interface in net.sourceforge.seqware.common.dao

ExperimentAttributeDAO interface.

ExperimentAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ExperimentAttributeDAOHibernate class.

ExperimentAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate

ExperimentAttributeFacadeREST - Class in io.seqware.webservice.generated.controller

ExperimentAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ExperimentAttributeFacadeREST

ExperimentController - Class in net.sourceforge.solexatools.webapp.controller

ExperimentController

ExperimentController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ExperimentController

Constructor for ExperimentController.

ExperimentController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.ExperimentController

Constructor for ExperimentController.

ExperimentDAO - Interface in net.sourceforge.seqware.common.dao

ExperimentDAO interface.

ExperimentDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ExperimentDAOHibernate class.

ExperimentDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

Constructor for ExperimentDAOHibernate.

ExperimentFacadeREST - Class in io.seqware.webservice.generated.controller

ExperimentFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ExperimentFacadeREST

ExperimentIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters

ExperimentIDFilter class.

ExperimentIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.ExperimentIDFilter

ExperimentIDResource - Class in net.sourceforge.seqware.webservice.resources.tables

ExperimentIDResource class.

ExperimentIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource

Constructor for ExperimentIDResource.

ExperimentLibraryDesign - Class in io.seqware.webservice.generated.model

ExperimentLibraryDesign() - Constructor for class io.seqware.webservice.generated.model.ExperimentLibraryDesign

ExperimentLibraryDesign(Integer) - Constructor for class io.seqware.webservice.generated.model.ExperimentLibraryDesign

ExperimentLibraryDesign - Class in net.sourceforge.seqware.common.model

ExperimentLibraryDesign class.

ExperimentLibraryDesign() - Constructor for class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Constructor for ExperimentLibraryDesign.

ExperimentLibraryDesignDAO - Interface in net.sourceforge.seqware.common.dao

ExperimentLibraryDesignDAO interface.

ExperimentLibraryDesignDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ExperimentLibraryDesignDAOHibernate class.

ExperimentLibraryDesignDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate

Constructor for ExperimentLibraryDesignDAOHibernate.

ExperimentLibraryDesignFacadeREST - Class in io.seqware.webservice.generated.controller

ExperimentLibraryDesignFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ExperimentLibraryDesignFacadeREST

ExperimentLibraryDesignList - Class in net.sourceforge.seqware.common.model.lists

ExperimentLibraryDesignList class.

ExperimentLibraryDesignList() - Constructor for class net.sourceforge.seqware.common.model.lists.ExperimentLibraryDesignList

Constructor for ExperimentLibraryDesignList.

ExperimentLibraryDesignResource - Class in net.sourceforge.seqware.webservice.resources.tables

ExperimentLibraryDesignResource class.

ExperimentLibraryDesignResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ExperimentLibraryDesignResource

Constructor for ExperimentResource.

ExperimentLibraryDesignService - Interface in net.sourceforge.seqware.common.business

ExperimentLibraryDesignService interface.

ExperimentLibraryDesignServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ExperimentLibraryDesignServiceImpl class.

ExperimentLibraryDesignServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl

Constructor for ExperimentLibraryDesignServiceImpl.

ExperimentLink - Class in io.seqware.webservice.generated.model

ExperimentLink() - Constructor for class io.seqware.webservice.generated.model.ExperimentLink

ExperimentLink(Integer) - Constructor for class io.seqware.webservice.generated.model.ExperimentLink

ExperimentLink - Class in net.sourceforge.seqware.common.model

ExperimentLink generated by hbm2java

ExperimentLink() - Constructor for class net.sourceforge.seqware.common.model.ExperimentLink

Constructor for ExperimentLink.

ExperimentLink(int, Experiment) - Constructor for class net.sourceforge.seqware.common.model.ExperimentLink

Constructor for ExperimentLink.

ExperimentLink(int, Experiment, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.ExperimentLink

Constructor for ExperimentLink.

ExperimentLinkDAO - Interface in net.sourceforge.seqware.common.dao

ExperimentLinkDAO interface.

ExperimentLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ExperimentLinkDAOHibernate class.

ExperimentLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate

ExperimentLinkFacadeREST - Class in io.seqware.webservice.generated.controller

ExperimentLinkFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ExperimentLinkFacadeREST

ExperimentList - Class in net.sourceforge.seqware.common.model.lists

ExperimentList class.

ExperimentList() - Constructor for class net.sourceforge.seqware.common.model.lists.ExperimentList

Constructor for ExperimentList.

ExperimentResource - Class in net.sourceforge.seqware.webservice.resources.tables

ExperimentResource class.

ExperimentResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource

Constructor for ExperimentResource.

ExperimentService - Interface in net.sourceforge.seqware.common.business

ExperimentService interface.

ExperimentServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ExperimentServiceImpl class.

ExperimentServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

Constructor for ExperimentServiceImpl.

ExperimentSetupController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController

ExperimentSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController

Constructor for ExperimentSetupController.

ExperimentSpotDesign - Class in io.seqware.webservice.generated.model

ExperimentSpotDesign() - Constructor for class io.seqware.webservice.generated.model.ExperimentSpotDesign

ExperimentSpotDesign(Integer) - Constructor for class io.seqware.webservice.generated.model.ExperimentSpotDesign

ExperimentSpotDesign - Class in net.sourceforge.seqware.common.model

ExperimentSpotDesign class.

ExperimentSpotDesign() - Constructor for class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Constructor for ExperimentSpotDesign.

ExperimentSpotDesignDAO - Interface in net.sourceforge.seqware.common.dao

ExperimentSpotDesignDAO interface.

ExperimentSpotDesignDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ExperimentSpotDesignDAOHibernate class.

ExperimentSpotDesignDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate

Constructor for ExperimentSpotDesignDAOHibernate.

ExperimentSpotDesignFacadeREST - Class in io.seqware.webservice.generated.controller

ExperimentSpotDesignFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ExperimentSpotDesignFacadeREST

ExperimentSpotDesignList - Class in net.sourceforge.seqware.common.model.lists

ExperimentSpotDesignList class.

ExperimentSpotDesignList() - Constructor for class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignList

Constructor for ExperimentSpotDesignList.

ExperimentSpotDesignReadSpec - Class in io.seqware.webservice.generated.model

ExperimentSpotDesignReadSpec() - Constructor for class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

ExperimentSpotDesignReadSpec(Integer) - Constructor for class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

ExperimentSpotDesignReadSpec - Class in net.sourceforge.seqware.common.model

ExperimentSpotDesignReadSpec class.

ExperimentSpotDesignReadSpec() - Constructor for class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Constructor for ExperimentSpotDesignReadSpec.

ExperimentSpotDesignReadSpecComparator - Class in net.sourceforge.seqware.common.model.comparator

ExperimentSpotDesignReadSpecComparator class.

ExperimentSpotDesignReadSpecComparator() - Constructor for class net.sourceforge.seqware.common.model.comparator.ExperimentSpotDesignReadSpecComparator

ExperimentSpotDesignReadSpecDAO - Interface in net.sourceforge.seqware.common.dao

ExperimentSpotDesignReadSpecDAO interface.

ExperimentSpotDesignReadSpecDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ExperimentSpotDesignReadSpecDAOHibernate class.

ExperimentSpotDesignReadSpecDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate

Constructor for ExperimentSpotDesignReadSpecDAOHibernate.

ExperimentSpotDesignReadSpecFacadeREST - Class in io.seqware.webservice.generated.controller

ExperimentSpotDesignReadSpecFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ExperimentSpotDesignReadSpecFacadeREST

ExperimentSpotDesignReadSpecList - Class in net.sourceforge.seqware.common.model.lists

ExperimentSpotDesignReadSpecList class.

ExperimentSpotDesignReadSpecList() - Constructor for class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignReadSpecList

Constructor for ExperimentSpotDesignReadSpecList.

ExperimentSpotDesignReadSpecResource - Class in net.sourceforge.seqware.webservice.resources.tables

ExperimentSpotDesignReadSpecResource class.

ExperimentSpotDesignReadSpecResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ExperimentSpotDesignReadSpecResource

Constructor for ExperimentResource.

ExperimentSpotDesignReadSpecService - Interface in net.sourceforge.seqware.common.business

ExperimentSpotDesignReadSpecService interface.

ExperimentSpotDesignReadSpecServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ExperimentSpotDesignReadSpecServiceImpl class.

ExperimentSpotDesignReadSpecServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl

Constructor for ExperimentSpotDesignReadSpecServiceImpl.

ExperimentSpotDesignResource - Class in net.sourceforge.seqware.webservice.resources.tables

ExperimentSpotDesignResource class.

ExperimentSpotDesignResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ExperimentSpotDesignResource

Constructor for ExperimentResource.

ExperimentSpotDesignService - Interface in net.sourceforge.seqware.common.business

ExperimentSpotDesignService interface.

ExperimentSpotDesignServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ExperimentSpotDesignServiceImpl class.

ExperimentSpotDesignServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl

Constructor for ExperimentSpotDesignServiceImpl.

ExperimentUpdateValidator - Class in net.sourceforge.solexatools.validation

ExperimentUpdateValidator class.

ExperimentUpdateValidator() - Constructor for class net.sourceforge.solexatools.validation.ExperimentUpdateValidator

ExperimentValidator - Class in net.sourceforge.solexatools.validation

ExperimentValidator class.

ExperimentValidator() - Constructor for class net.sourceforge.solexatools.validation.ExperimentValidator

Constructor for ExperimentValidator.

exportINI(PluginRunnerET, List<Integer>) - Method in class io.seqware.pipeline.plugins.sanity.ProvidedBundleCLIUserPhase5

exportINI(PluginRunnerET, List<Integer>) - Method in class io.seqware.pipeline.plugins.sanity.ProvidedBundleUserPhase5

EXTENDED_TEST_DB_HOST_KEY - Static variable in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator

EXTENDED_TEST_DB_NAME_KEY - Static variable in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator

EXTENDED_TEST_PASSWORD_KEY - Static variable in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator

EXTENDED_TEST_USERNAME_KEY - Static variable in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator

ExtendedTestDatabaseCreator - Class in net.sourceforge.seqware.pipeline.plugins

This class controls configuration of the database used for extended integration tests.

ExtendedTestDatabaseCreator() - Constructor for class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator

extractSwid(String) - Static method in class net.sourceforge.seqware.pipeline.plugins.ITUtility

extractValueFrom(String, String) - Static method in class net.sourceforge.seqware.pipeline.plugins.ITUtility

F

FAILURE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant FAILURE=15

failWorkflow(int) - Static method in class io.seqware.WorkflowRuns

Fastq(File, String, String, int) - Static method in class net.sourceforge.seqware.common.util.filetools.validate.Validate

Fastq.

fatal(Object) - Static method in class net.sourceforge.seqware.common.util.Log

See Category.fatal(Object).

fatal(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log

See Category.fatal(Object,Throwable).

featureNotImplemented() - Static method in class net.sourceforge.seqware.common.module.ReturnValue

featureNotImplemented.

fields - Variable in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

fields - Variable in class net.sourceforge.seqware.webservice.resources.BasicResource

fields - Variable in class net.sourceforge.seqware.webservice.resources.BasicRestlet

fieldsConfirmed(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

File - Class in io.seqware.webservice.generated.model

File() - Constructor for class io.seqware.webservice.generated.model.File

File(Integer) - Constructor for class io.seqware.webservice.generated.model.File

File(Integer, String) - Constructor for class io.seqware.webservice.generated.model.File

File - Class in net.sourceforge.seqware.common.model

File class.

File() - Constructor for class net.sourceforge.seqware.common.model.File

Constructor for File.

file(File, String, boolean) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

FILE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

FILE_DESCRIPTION - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

FILE_EXPERIMENT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_EXPERIMENT_NAME="f_exp_name"

FILE_EXPERIMENT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_EXPERIMENT_NAME="f_exp_name"

FILE_EXPERIMENT_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_EXPERIMENT_SWID="f_exp_swid"

FILE_EXPERIMENT_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_EXPERIMENT_SWID="f_exp_swid"

FILE_FILE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_FILE="f_file"

FILE_FILE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_FILE="f_file"

FILE_IUS - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_IUS="f_ius"

FILE_IUS - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_IUS="f_ius"

FILE_IUS_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_IUS_NAME="f_ius_name"

FILE_IUS_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_IUS_SWID="f_ius_swid"

FILE_IUS_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_IUS_SWID="f_ius_swid"

FILE_IUS_TAG - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_IUS_TAG="f_ius_tag"

FILE_IUS_TAG - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_IUS_TAG="f_ius_tag"

FILE_LANE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_LANE="f_lane"

FILE_LANE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_LANE="f_lane"

FILE_LANE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_LANE_NAME="f_lane_name"

FILE_LANE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_LANE_NAME="f_lane_name"

FILE_LANE_NUMBER - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_LANE_NUMBER="f_lane_num"

FILE_LANE_NUMBER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_LANE_NUMBER="f_lane_num"

FILE_LANE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_LANE_SWID="f_lane_swid"

FILE_LANE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_LANE_SWID="f_lane_swid"

FILE_LIBRARY - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_LIBRARY="f_library"

FILE_LIBRARY - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_LIBRARY="f_library"

FILE_MD5SUM - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

FILE_META_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_META_TYPE="f_file_meta"

FILE_META_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_META_TYPE="f_file_meta"

FILE_PARENT_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_PARENT_SAMPLE_NAME="f_sample_name"

FILE_PARENT_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_PARENT_SAMPLE_NAME="f_sample_name"

FILE_PARENT_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_PARENT_SAMPLE_SWID="f_sample_swid"

FILE_PARENT_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_PARENT_SAMPLE_SWID="f_sample_swid"

FILE_PATH - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

FILE_PATH - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_PATH="f_file_path"

FILE_PATH - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_PATH="f_file_path"

FILE_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant

Constant FILE_PREFIX="fl_"

FILE_PROCESSING_ALG - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_PROCESSING_ALG="f_processing_alg"

FILE_PROCESSING_ALG - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_PROCESSING_ALG="f_processing_alg"

FILE_PROCESSING_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_PROCESSING_SWID="f_processing_swid"

FILE_PROCESSING_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_PROCESSING_SWID="f_processing_swid"

FILE_RUN_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_RUN_NAME="f_run_name"

FILE_RUN_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_RUN_NAME="f_run_name"

FILE_RUN_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_RUN_SWID="f_run_swid"

FILE_RUN_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_RUN_SWID="f_run_swid"

FILE_SAMPLE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_SAMPLE="f_sample"

FILE_SAMPLE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_SAMPLE="f_sample"

FILE_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_SAMPLE_NAME="f_child_sample_name"

FILE_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_SAMPLE_NAME="f_child_sample_name"

FILE_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_SAMPLE_SWID="f_child_sample_swid"

FILE_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_SAMPLE_SWID="f_child_sample_swid"

FILE_SEQUENCER_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_SEQUENCER_NAME="f_seqrun_name"

FILE_SEQUENCER_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_SEQUENCER_NAME="f_seqrun_name"

FILE_SEQUENCER_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_SEQUENCER_SWID="f_seqrun_swid"

FILE_SEQUENCER_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_SEQUENCER_SWID="f_seqrun_swid"

FILE_SIZE - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

FILE_STUDY_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_STUDY_SWID="f_study_swid"

FILE_STUDY_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_STUDY_SWID="f_study_swid"

FILE_STUDY_TITLE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_STUDY_TITLE="f_study_title"

FILE_STUDY_TITLE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_STUDY_TITLE="f_study_title"

FILE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant FILE_SWA="Header.FILE_SWA.getTitle()"

FILE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_SWID="f_file_swid"

FILE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_SWID="f_file_swid"

FILE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

FILE_TEMPLATE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_TEMPLATE="f_template"

FILE_TEMPLATE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_TEMPLATE="f_template"

FILE_TISSUE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_TISSUE="f_tissue"

FILE_TISSUE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_TISSUE="f_tissue"

FILE_WF_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_WF_NAME="f_wf_name"

FILE_WF_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_WF_NAME="f_wf_name"

FILE_WF_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_WF_SWID="f_wf_swid"

FILE_WF_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_WF_SWID="f_wf_swid"

FILE_WF_VERSION - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant FILE_WF_VERSION="f_wf_version"

FILE_WF_VERSION - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant FILE_WF_VERSION="f_wf_version"

FileAttribute - Class in io.seqware.webservice.generated.model

FileAttribute() - Constructor for class io.seqware.webservice.generated.model.FileAttribute

FileAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.FileAttribute

FileAttribute(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.FileAttribute

FileAttribute - Class in net.sourceforge.seqware.common.model

FileAttribute() - Constructor for class net.sourceforge.seqware.common.model.FileAttribute

Constructor for FileAttribute.

FileAttribute(Integer) - Constructor for class net.sourceforge.seqware.common.model.FileAttribute

Constructor for FileAttribute.

FileAttributeDAO - Interface in net.sourceforge.seqware.common.dao

FileAttributeDAO interface.

FileAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

FileAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate

FileAttributeFacadeREST - Class in io.seqware.webservice.generated.controller

FileAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.FileAttributeFacadeREST

FileAttributeResource - Interface in net.sourceforge.seqware.webservice.resources.tables

FileAttributeResource interface.

FileAttributeServerResource - Class in net.sourceforge.seqware.webservice.resources.tables

FileAttributeServerResource class.

FileAttributeServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource

Constructor for FileAttributeServerResource.

FileAttributeService - Interface in net.sourceforge.seqware.common.business

FileAttributeService interface.

FileAttributeServiceImpl - Class in net.sourceforge.seqware.common.business.impl

FileAttributeServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl

FileAttributesResource - Interface in net.sourceforge.seqware.webservice.resources.tables

FileAttributesResource interface.

FileAttributesServerResource - Class in net.sourceforge.seqware.webservice.resources.tables

FileAttributesServerResource class.

FileAttributesServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileAttributesServerResource

Constructor for FileAttributesServerResource.

FileChildLimitedWorkflowRunsResource - Class in net.sourceforge.seqware.webservice.resources.tables

This resource will pull back the workflow runs that are generated from a particular file.

FileChildLimitedWorkflowRunsResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileChildLimitedWorkflowRunsResource

Constructor for FileChildWorkflowRunsResource.

FileChildWorkflowRunsResource - Class in net.sourceforge.seqware.webservice.resources.tables

This resource will pull back the workflow runs that are generated from a particular file.

FileChildWorkflowRunsResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource

Constructor for FileChildWorkflowRunsResource.

FileChildWorkflowRunsResource.SEARCH_TYPE - Enum in net.sourceforge.seqware.webservice.resources.tables

FileController - Class in net.sourceforge.solexatools.webapp.controller

LaneController

FileController() - Constructor for class net.sourceforge.solexatools.webapp.controller.FileController

Constructor for FileController.

FileController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.FileController

Constructor for FileController.

FileDAO - Interface in net.sourceforge.seqware.common.dao

FileDAO interface.

FileDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

FileDAOHibernate class.

FileDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

Constructor for FileDAOHibernate.

FileDto - Class in net.sourceforge.seqware.webservice.dto

FileDto() - Constructor for class net.sourceforge.seqware.webservice.dto.FileDto

FILEEMPTY - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant FILEEMPTY=12

fileExistsAndExecutable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

fileExistsAndExecutable.

fileExistsAndNotEmpty(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

fileExistsAndNotEmpty.

fileExistsAndReadable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

fileExistsAndReadable.

FileFacadeREST - Class in io.seqware.webservice.generated.controller

FileFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.FileFacadeREST

FileFinder - Class in net.sourceforge.solexatools.util

FileFinder class.

FileFinder() - Constructor for class net.sourceforge.solexatools.util.FileFinder

Constructor for FileFinder.

FileFinder(Pattern) - Constructor for class net.sourceforge.solexatools.util.FileFinder

Constructor for FileFinder.

FileIDResource - Class in net.sourceforge.seqware.webservice.resources.tables

FileIDResource class.

FileIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileIDResource

Constructor for FileIDResource.

FileLinker - Class in net.sourceforge.seqware.pipeline.plugins

FileLinker class.

FileLinker() - Constructor for class net.sourceforge.seqware.pipeline.plugins.FileLinker

FileLinkerLine - Class in net.sourceforge.seqware.pipeline.plugins.filelinker

FileLinkerLine() - Constructor for class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

FileLinkerLineException - Exception in net.sourceforge.seqware.pipeline.plugins.filelinker

FileLinkerLineException(String) - Constructor for exception net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLineException

FileLinkerParser - Class in net.sourceforge.seqware.pipeline.plugins.filelinker

FileLinkerParser() - Constructor for class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerParser

fileLinkReport() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl

Runs the ValidationReportService.fileLinkReport(List) including all files in the SeqWare meta db.

fileLinkReport(List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl

Every file must be associated with at least one processing node and this node in turn must be linked (either directly or through a parent) to one of the following: sequencer_run, lane, ius, sample, experiment or study.

fileLinkReport() - Method in interface net.sourceforge.seqware.common.business.ValidationReportService

Runs the ValidationReportService.fileLinkReport(List) including all files in the SeqWare meta db.

fileLinkReport(List<Integer>) - Method in interface net.sourceforge.seqware.common.business.ValidationReportService

Every file must be associated with at least one processing node and this node in turn must be linked (either directly or through a parent) to one of the following: sequencer_run, lane, ius, sample, experiment or study.

FileLinkReportResource - Class in net.sourceforge.seqware.webservice.resources.tables

FileLinkReportResource class.

FileLinkReportResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileLinkReportResource

Constructor for FileLinkReportResource.

FileList - Class in net.sourceforge.seqware.common.model.lists

FileList class.

FileList() - Constructor for class net.sourceforge.seqware.common.model.lists.FileList

Constructor for FileList.

FileMetadata - Class in net.sourceforge.seqware.common.module

This is a simple data structure to represent a file and it's metadata.

FileMetadata() - Constructor for class net.sourceforge.seqware.common.module.FileMetadata

FileMetadata(String, String) - Constructor for class net.sourceforge.seqware.common.module.FileMetadata

FileMetadata(String, String, String, String) - Constructor for class net.sourceforge.seqware.common.module.FileMetadata

fileName - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

FILENOTEXECUTABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant FILENOTEXECUTABLE=10

FILENOTREADABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant FILENOTREADABLE=4

FILENOTWRITABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant FILENOTWRITABLE=5

FileProvenanceParam - Enum in net.sourceforge.seqware.common.model

fileProvenanceReport(Map<FileProvenanceParam, List<String>>, Writer) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Retrieves the file provenance report, writing it to the specified output stream as a TSV.

fileProvenanceReport(Map<FileProvenanceParam, List<String>>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Retrieves the file provenance report.

fileProvenanceReport(Map<FileProvenanceParam, List<String>>, Writer) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

fileProvenanceReport(Map<FileProvenanceParam, List<String>>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

fileProvenanceReport(Map<FileProvenanceParam, List<String>>, Writer) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

fileProvenanceReport(Map<FileProvenanceParam, List<String>>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

fileProvenanceReport(Map<FileProvenanceParam, List<String>>, Writer) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

fileProvenanceReport(Map<FileProvenanceParam, List<String>>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

FileProvenanceReporter - Class in net.sourceforge.seqware.pipeline.plugins.fileprovenance

Lightweight wrapper for file provenance report

FileProvenanceReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.fileprovenance.FileProvenanceReporter

fileProvenanceReportTrigger() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Triggers the file provenance report, this is a costly operation so it should be scheduled via a cron or similar

fileProvenanceReportTrigger() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

fileProvenanceReportTrigger() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

fileProvenanceReportTrigger() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

FileProvenanceResource - Class in net.sourceforge.seqware.webservice.resources.queries

FileProvenanceResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.FileProvenanceResource

FileReport - Class in io.seqware.webservice.generated.model

FileReport() - Constructor for class io.seqware.webservice.generated.model.FileReport

FileReport(Integer) - Constructor for class io.seqware.webservice.generated.model.FileReport

FileReportDAO - Interface in net.sourceforge.seqware.common.dao

FileReportDAO interface.

FileReportDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

FileReportDAOHibernate class.

FileReportDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate

FileReportFacadeREST - Class in io.seqware.webservice.generated.controller

FileReportFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.FileReportFacadeREST

FileReportRow - Class in net.sourceforge.seqware.common.model

FileReportRow class.

FileReportRow() - Constructor for class net.sourceforge.seqware.common.model.FileReportRow

FileReportService - Interface in net.sourceforge.seqware.common.business

FileReportService interface.

FileReportServiceImpl - Class in net.sourceforge.seqware.common.business.impl

FileReportServiceImpl class.

FileReportServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl

FileResource - Class in net.sourceforge.seqware.webservice.resources.tables

FileResource class.

FileResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileResource

Constructor for FileResource.

fileReverseHierarchyDisplay(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl

Produces a text representation of a reverse hierarchy tree starting at a file (indicated by the provided fileSwa).

fileReverseHierarchyDisplay(Integer) - Method in interface net.sourceforge.seqware.common.business.ValidationReportService

Produces a text representation of a reverse hierarchy tree starting at a file (indicated by the provided fileSwa).

FileReverseHierarchyDisplayResource - Class in net.sourceforge.seqware.webservice.resources.tables

FileReverseHierarchyDisplayResource class.

FileReverseHierarchyDisplayResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileReverseHierarchyDisplayResource

Constructor for FileReverseHierarchyDisplayResource.

files - Variable in class net.sourceforge.seqware.common.module.ReturnValue

filesArray - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle

filesArray - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

FileService - Interface in net.sourceforge.seqware.common.business

FileService interface.

FileServiceImpl - Class in net.sourceforge.seqware.common.business.impl

FileServiceImpl class.

FileServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileServiceImpl

Constructor for FileServiceImpl.

FileSetupController - Class in net.sourceforge.solexatools.webapp.controller

FileSetupController class.

FileSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.FileSetupController

filesFromExperiment(Experiment, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

FIXME: notice processings directly attached to study aren't examined!

filesFromIUS(IUS, Experiment, Sample, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

filesFromIUS.

filesFromLane(Lane, Experiment, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

filesFromLane.

filesFromSample(Sample, Experiment, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

filesFromSample.

filesFromStudy(Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

FIXME: notice processings directly attached to study aren't examined!

filesFromStudy(Study) - Method in class net.sourceforge.seqware.common.hibernate.PropagateOwnership

filesFromStudy.

fileString2FileMetadata(String) - Static method in class net.sourceforge.seqware.pipeline.plugins.Metadata

FileTools - Class in net.sourceforge.seqware.common.util.filetools

FileTools class.

FileTools() - Constructor for class net.sourceforge.seqware.common.util.filetools.FileTools

FileTools.LocalhostPair - Class in net.sourceforge.seqware.common.util.filetools

FileTools.LocalhostPair(String, ReturnValue) - Constructor for class net.sourceforge.seqware.common.util.filetools.FileTools.LocalhostPair

FileType - Class in io.seqware.webservice.generated.model

FileType() - Constructor for class io.seqware.webservice.generated.model.FileType

FileType(Integer) - Constructor for class io.seqware.webservice.generated.model.FileType

FileType - Class in net.sourceforge.seqware.common.model

FileType class.

FileType() - Constructor for class net.sourceforge.seqware.common.model.FileType

Constructor for FileType.

FILETYPE_ALL - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant FILETYPE_ALL="all"

FileTypeDAO - Interface in net.sourceforge.seqware.common.dao

FileTypeDAO interface.

FileTypeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

FileTypeDAOHibernate class.

FileTypeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate

Constructor for FileTypeDAOHibernate.

FileTypeFacadeREST - Class in io.seqware.webservice.generated.controller

FileTypeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.FileTypeFacadeREST

FileTypeService - Interface in net.sourceforge.seqware.common.business

FileTypeService interface.

FileTypeServiceImpl - Class in net.sourceforge.seqware.common.business.impl

FileTypeServiceImpl class.

FileTypeServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl

Constructor for FileTypeServiceImpl.

FileUploadService - Interface in net.sourceforge.seqware.common.business

FileUploadService interface.

FileUploadServiceImpl - Class in net.sourceforge.seqware.common.business.impl

FileUploadServiceImpl class.

FileUploadServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

Constructor for FileUploadServiceImpl.

FileValidator - Class in net.sourceforge.solexatools.validation

FileValidator class.

FileValidator() - Constructor for class net.sourceforge.solexatools.validation.FileValidator

Constructor for FileValidator.

fillWorkflowProcessingMap(Processing, Map<WorkflowRun, Set<Processing>>) - Static method in class net.sourceforge.solexatools.util.ControllerUtil

fillWorkflowProcessingMap.

fillWorkflowProcessingMap(Processing, Map<WorkflowRun, Set<Processing>>) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

fillWorkflowProcessingMap.

filterReturnValues(List<ReturnValue>, String, String, boolean, boolean, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

filterReturnValues.

find(Integer) - Method in class io.seqware.webservice.controller.UtilityREST

Returns a tuple describing the class and accession given only an accession

find(Object) - Method in class io.seqware.webservice.generated.controller.AbstractFacade

find(Integer) - Method in class io.seqware.webservice.generated.controller.ExpenseAttributeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ExpenseFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentAttributeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentLibraryDesignFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentLinkFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignReadSpecFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.FileAttributeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.FileFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.FileReportFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.FileTypeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.InvoiceAttributeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.InvoiceFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.IusAttributeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.IusFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.IusLinkFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.IusWorkflowRunsFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.LaneAttributeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.LaneFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.LaneLinkFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.LaneTypeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.LaneWorkflowRunsFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.LibrarySelectionFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.LibrarySourceFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.LibraryStrategyFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.OrganismFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.PlatformFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingAttributeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingExperimentsFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingFilesFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingIusFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingLanesFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingRelationshipFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingSamplesFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingSequencerRunsFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingStudiesFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.RegistrationFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.SampleAttributeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.SampleFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.SampleLinkFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.SampleRelationshipFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.SampleReportFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.SampleSearchAttributeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.SampleSearchFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.SequencerRunAttributeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.SequencerRunFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ShareExperimentFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ShareFileFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ShareLaneFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ShareProcessingFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ShareSampleFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ShareStudyFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.ShareWorkflowRunFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.StudyAttributeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.StudyFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.StudyLinkFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.StudyTypeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowAttributeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowParamFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowParamValueFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowRunAttributeFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowRunFacadeREST

find(Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowRunParamFacadeREST

find(String, Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

find.

find(String, Integer, String) - Method in interface net.sourceforge.seqware.common.business.IUSService

find.

find(String, Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

find.

find(String, Integer, String) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

find.

find_JSON(Class<T>, String) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

find_JSON_rdelete(Class, String) - Method in class io.seqware.webservice.client.SeqWareWebServiceClient

find_XML(Class<T>, String) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

findAll() - Method in class io.seqware.webservice.generated.controller.AbstractFacade

findAll() - Method in class io.seqware.webservice.generated.controller.ExpenseAttributeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ExpenseFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ExperimentAttributeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ExperimentFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ExperimentLibraryDesignFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ExperimentLinkFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignReadSpecFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.FileAttributeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.FileFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.FileReportFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.FileTypeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.InvoiceAttributeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.InvoiceFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.IusAttributeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.IusFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.IusLinkFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.IusWorkflowRunsFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.LaneAttributeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.LaneFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.LaneLinkFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.LaneTypeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.LaneWorkflowRunsFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.LibrarySelectionFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.LibrarySourceFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.LibraryStrategyFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.OrganismFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.PlatformFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ProcessingAttributeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ProcessingExperimentsFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ProcessingFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ProcessingFilesFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ProcessingIusFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ProcessingLanesFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ProcessingRelationshipFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ProcessingSamplesFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ProcessingSequencerRunsFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ProcessingStudiesFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.RegistrationFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.SampleAttributeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.SampleFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.SampleLinkFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.SampleRelationshipFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.SampleReportFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.SampleSearchAttributeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.SampleSearchFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.SequencerRunAttributeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.SequencerRunFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ShareExperimentFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ShareFileFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ShareLaneFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ShareProcessingFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ShareSampleFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ShareStudyFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.ShareWorkflowRunFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.StudyAttributeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.StudyFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.StudyLinkFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.StudyTypeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.WorkflowAttributeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.WorkflowFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.WorkflowParamFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.WorkflowParamValueFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.WorkflowRunAttributeFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.WorkflowRunFacadeREST

findAll() - Method in class io.seqware.webservice.generated.controller.WorkflowRunParamFacadeREST

findAll(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO

findAll.

findAll(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO

findAll.

findAll(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate

findAll.

findAll(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate

findAll.

findAll(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate

findAll.

findAll(IUS) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO

findAll.

findAll(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate

findAll.

findAll(Lane) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO

findAll.

findAll(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate

findAll.

findAll(Lane) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO

findAll.

findAll(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate

findAll.

findAll(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate

findAll.

findAll(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate

findAll.

findAll(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate

findAll.

findAll(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate

findAll.

findAll(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate

findAll.

findAll(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO

findAll.

findAll(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO

findAll.

findAll(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO

findAll.

findAll(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO

findAll.

findAll(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO

findAll.

findAll(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO

findAll.

findAll(String) - Method in class net.sourceforge.solexatools.util.FileFinder

findAll.

findAll(String, String) - Method in class net.sourceforge.solexatools.util.FileFinder

findAll.

findAll_JSON(Class<T>) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

findAll_XML(Class<T>) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

FindAllTheFiles - Class in net.sourceforge.seqware.common.hibernate

Should only be used for one query and then discarded and re-instantiated.

FindAllTheFiles() - Constructor for class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

FindAllTheFiles.Header - Enum in net.sourceforge.seqware.common.hibernate

findBelongsToStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

findBelongsToStudy.

findBelongsToStudy(Study) - Method in interface net.sourceforge.seqware.common.business.IUSService

findBelongsToStudy.

findBelongsToStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

findBelongsToStudy.

findBelongsToStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

findBelongsToStudy.

findBundleInfo(File) - Static method in class net.sourceforge.seqware.pipeline.bundle.Bundle

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.FileService

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

findByCriteria.

findByCriteria(String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

findByCriteria.

findByCriteria(String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.IUSService

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.LaneService

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.SampleService

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService

findByCriteria.

findByCriteria(String) - Method in interface net.sourceforge.seqware.common.business.StudyService

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

findByCriteria.

findByCriteria(String) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

findByCriteria.

findByCriteria(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

findByCriteria.

findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

findByCriteria.

findByCriteria(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

findByCriteria.

findByCriteria(String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

findByCriteria.

findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

findByCriteria.

findByCriteria(String) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

findByCriteria.

findByEmailAddress(String) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl

findByEmailAddress.

findByEmailAddress(String) - Method in interface net.sourceforge.seqware.common.business.RegistrationService

findByEmailAddress.

findByEmailAddress(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate

findByEmailAddress.

findByEmailAddress(String) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO

findByEmailAddress.

findByEmailAddressAndPassword(String, String) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl

findByEmailAddressAndPassword.

findByEmailAddressAndPassword(String, String) - Method in interface net.sourceforge.seqware.common.business.RegistrationService

findByEmailAddressAndPassword.

findByEmailAddressAndPassword(String, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate

findByEmailAddressAndPassword.

findByEmailAddressAndPassword(String, String) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO

findByEmailAddressAndPassword.

findByFilePath(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

findByFilePath.

findByFilePath(String) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

findByFilePath.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.FileTypeService

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

findByID.

findById(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl

findById.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.InvoiceService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.OrganismService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.PlatformService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

findByID.

findById(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleSearchService

findById.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareFileService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileTypeDAO

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

findByID.

findById(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate

findById.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate

findByID.

findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

findByID.

findById(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleSearchDAO

findById.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO

findByID.

findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

findByID.

findByIDOnlyWithRunningWR(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

findByIDOnlyWithRunningWR.

findByIDOnlyWithRunningWR(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

findByIDOnlyWithRunningWR.

findByIDWithIUS(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

findByIDWithIUS.

findByIDWithIUS(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

findByIDWithIUS.

findByIDWithIUSAndRunningWR(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

findByIDWithIUSAndRunningWR.

findByIDWithIUSAndRunningWR(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

findByIDWithIUSAndRunningWR.

findByIDWithParams(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

findByIDWithParams.

findByIDWithParams(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

findByIDWithParams.

findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

findByName.

findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

findByName.

findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

findByName.

findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl

findByName.

findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

findByName.

findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

findByName.

findByName(String) - Method in interface net.sourceforge.seqware.common.business.LaneService

findByName.

findByName(String) - Method in interface net.sourceforge.seqware.common.business.SampleService

findByName.

findByName(String) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

findByName.

findByName(String) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService

findByName.

findByName(String) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

findByName.

findByName(String) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

findByName.

findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

findByName.

findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

findByName.

findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

findByName.

findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate

findByName.

findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

findByName.

findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

findByName.

findByName(String) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

findByName.

findByName(String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

findByName.

findByName(String) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

findByName.

findByName(String) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO

findByName.

findByName(String) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

findByName.

findByName(String) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

findByName.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

findByOwnerID.

findByOwnerId(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService

findByOwnerId.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

findByOwnerID.

findByOwnerId(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

findByOwnerId.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareFileService

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

findByOwnerID.

findByOwnerId(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

findByOwnerId.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

findByOwnerID.

findByOwnerId(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

findByOwnerId.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

findByOwnerID.

findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

findByOwnerID.

findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

findByOwnerID.

findByPath(String) - Method in interface net.sourceforge.seqware.common.business.FileService

findByPath.

findByPath(String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

findByPath.

findByPath(String) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

findByPath.

findByPath(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

findByPath.

findByProcessingExperiment(Processing, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl

findByProcessingExperiment.

findByProcessingExperiment(Processing, Experiment) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService

findByProcessingExperiment.

findByProcessingExperiment(Processing, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate

findByProcessingExperiment.

findByProcessingExperiment(Processing, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO

findByProcessingExperiment.

findByProcessingIUS(Processing, IUS) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl

findByProcessingIUS.

findByProcessingIUS(Processing, IUS) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService

findByProcessingIUS.

findByProcessingIUS(Processing, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate

findByProcessingIUS.

findByProcessingIUS(Processing, IUS) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO

findByProcessingIUS.

findByProcessingLane(Processing, Lane) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl

findByProcessingLane.

findByProcessingLane(Processing, Lane) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService

findByProcessingLane.

findByProcessingLane(Processing, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate

findByProcessingLane.

findByProcessingLane(Processing, Lane) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO

findByProcessingLane.

findByProcessings(Processing, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl

findByProcessings.

findByProcessings(Processing, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService

findByProcessings.

findByProcessings(Processing, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate

findByProcessings.

findByProcessings(Processing, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO

findByProcessings.

findByProcessingSample(Processing, Sample) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl

findByProcessingSample.

findByProcessingSample(Processing, Sample) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService

findByProcessingSample.

findByProcessingSample(Processing, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate

findByProcessingSample.

findByProcessingSample(Processing, Sample) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO

findByProcessingSample.

findByProcessingSequencerRun(Processing, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl

findByProcessingSequencerRun.

findByProcessingSequencerRun(Processing, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService

findByProcessingSequencerRun.

findByProcessingSequencerRun(Processing, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate

findByProcessingSequencerRun.

findByProcessingSequencerRun(Processing, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO

findByProcessingSequencerRun.

findByProcessingStudy(Processing, Study) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl

findByProcessingStudy.

findByProcessingStudy(Processing, Study) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService

findByProcessingStudy.

findByProcessingStudy(Processing, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate

findByProcessingStudy.

findByProcessingStudy(Processing, Study) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO

findByProcessingStudy.

findByStudyIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl

findByStudyIdAndRegistrationId.

findByStudyIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService

findByStudyIdAndRegistrationId.

findByStudyIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate

findByStudyIdAndRegistrationId.

findByStudyIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO

findByStudyIdAndRegistrationId.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

findBySWAccession.

findBySWAccession(Long) - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl

Returns library matching given SeqWare Accession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.InvoiceService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService

findBySWAccession.

findBySWAccession(Long) - Method in interface net.sourceforge.seqware.common.business.LibraryService

Returns library matching given SeqWare Accession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareFileService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

findBySWAccession.

findBySWAccession(Long) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate

Returns library matching given SeqWare Accesssion.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

findBySWAccession.

findBySWAccession(Long) - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO

Returns library matching given SeqWare Accesssion.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

findBySWAccession.

findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

findBySWAccession.

findByTitle(String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

findByTitle.

findByTitle(String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

findByTitle.

findByTitle(String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

findByTitle.

findByTitle(String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

findByTitle.

findByTitle(String) - Method in interface net.sourceforge.seqware.common.business.SampleService

findByTitle.

findByTitle(String) - Method in interface net.sourceforge.seqware.common.business.StudyService

findByTitle.

findByTitle(String) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

findByTitle.

findByTitle(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

findByTitle.

findByTitle(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

findByTitle.

findByTitle(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

findByTitle.

findByTitle(String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

findByTitle.

findByTitle(String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

findByTitle.

findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl

findByWorkflowRunIdAndRegistrationId.

findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService

findByWorkflowRunIdAndRegistrationId.

findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate

findByWorkflowRunIdAndRegistrationId.

findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO

findByWorkflowRunIdAndRegistrationId.

FindChildUtil - Class in net.sourceforge.solexatools.util

FindChildUtil class.

FindChildUtil() - Constructor for class net.sourceforge.solexatools.util.FindChildUtil

findDirectories(String) - Method in class net.sourceforge.solexatools.util.FileFinder

findDirectories.

findDirectories(String, String) - Method in class net.sourceforge.solexatools.util.FileFinder

findDirectories.

findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

findFiles.

findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

findFiles.

findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

findFiles.

findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

findFiles.

findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService

findFiles.

findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService

findFiles.

findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService

findFiles.

findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

findFiles.

findFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

findFiles.

findFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

findFiles.

findFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

findFiles.

findFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

findFiles.

findFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

findFiles.

findFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

findFiles.

findFiles(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport

findFiles(String) - Method in class net.sourceforge.solexatools.util.FileFinder

findFiles.

findFiles(String, String) - Method in class net.sourceforge.solexatools.util.FileFinder

findFiles.

findFilesAssociatedWithASample(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

findFilesAssociatedWithASample.

findFilesAssociatedWithASample(String, boolean) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

findFilesAssociatedWithASample.

findFilesAssociatedWithASample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

findFilesAssociatedWithASample.

findFilesAssociatedWithASample(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

findFilesAssociatedWithASample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

findFilesAssociatedWithASample.

findFilesAssociatedWithASample(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

findFilesAssociatedWithASample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

findFilesAssociatedWithASample.

findFilesAssociatedWithASample(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

findFilesAssociatedWithASequencerRun(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

findFilesAssociatedWithASequencerRun.

findFilesAssociatedWithASequencerRun(String, boolean) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

findFilesAssociatedWithASequencerRun.

findFilesAssociatedWithASequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

findFilesAssociatedWithASequencerRun.

findFilesAssociatedWithASequencerRun(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

findFilesAssociatedWithASequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

findFilesAssociatedWithASequencerRun.

findFilesAssociatedWithASequencerRun(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

findFilesAssociatedWithASequencerRun(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

findFilesAssociatedWithASequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

findFilesAssociatedWithASequencerRun.

findFilesAssociatedWithAStudy(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

findFilesAssociatedWithAStudy.

findFilesAssociatedWithAStudy(String, boolean) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Somewhat misnamed for now, this can return a mix of files and bare-nodes in the database hierarchy resulting from FileAllTheFiles.requireFiles=false

findFilesAssociatedWithAStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

findFilesAssociatedWithAStudy.

findFilesAssociatedWithAStudy(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

findFilesAssociatedWithAStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

findFilesAssociatedWithAStudy.

findFilesAssociatedWithAStudy(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

findFilesAssociatedWithAStudy(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

findFilesAssociatedWithAStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

findFilesAssociatedWithAStudy.

findFirstWorkflowClass(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowClassFinder

find the first .class in the clazzPath This has been modified to locate a specific class.

findFor(Sample, WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

findFor.

findFor(Sample) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

findFor.

findFor(Sample, WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

findFor.

findFor(Sample) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

findFor.

findIus() - Method in interface net.sourceforge.seqware.webservice.resources.tables.IusSearchResource

Locate IUS by sequencer run name, lane number and optionally sample name.

findIus() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusSearchServerResource

Locate IUS by sequencer run name, lane number and optionally sample name.

findOrganismId(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

findParents(Collection<Processing>, int, boolean) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport

findRange(int[]) - Method in class io.seqware.webservice.generated.controller.AbstractFacade

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ExpenseAttributeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ExpenseFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentAttributeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentLibraryDesignFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentLinkFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignReadSpecFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.FileAttributeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.FileFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.FileReportFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.FileTypeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.InvoiceAttributeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.InvoiceFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.IusAttributeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.IusFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.IusLinkFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.IusWorkflowRunsFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.LaneAttributeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.LaneFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.LaneLinkFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.LaneTypeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.LaneWorkflowRunsFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.LibrarySelectionFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.LibrarySourceFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.LibraryStrategyFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.OrganismFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.PlatformFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingAttributeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingExperimentsFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingFilesFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingIusFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingLanesFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingRelationshipFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingSamplesFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingSequencerRunsFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingStudiesFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.RegistrationFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.SampleAttributeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.SampleFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.SampleLinkFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.SampleRelationshipFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.SampleReportFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.SampleSearchAttributeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.SampleSearchFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.SequencerRunAttributeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.SequencerRunFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ShareExperimentFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ShareFileFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ShareLaneFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ShareProcessingFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ShareSampleFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ShareStudyFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.ShareWorkflowRunFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.StudyAttributeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.StudyFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.StudyLinkFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.StudyTypeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowAttributeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowParamFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowParamValueFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowRunAttributeFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowRunFacadeREST

findRange(Integer, Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowRunParamFacadeREST

findRange_JSON(Class<T>, String, String) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

findRange_XML(Class<T>, String, String) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

findRecursive(Integer, String) - Method in class io.seqware.webservice.controller.CustomWorkflowRunFacadeREST

Returns the list of potential victims for a deletion operation

FindRootUtil - Class in net.sourceforge.solexatools.util

FindRootUtil class.

FindRootUtil() - Constructor for class net.sourceforge.solexatools.util.FindRootUtil

findRunsForIUS(IUS) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

findRunsForIUS.

findRunsForIUS(IUS) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

findRunsForIUS.

findRunsForIUS(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

findRunsForIUS.

findRunsForIUS(IUS) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

findRunsForIUS.

findRunsForSample(Sample) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

Find all the workflow runs for the specific sample.

findRunsForSample(Sample) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

Find all the workflow runs for the specific sample.

findTupleByAccession(String) - Method in class io.seqware.webservice.client.SeqWareWebServiceClient

findValueByID(WorkflowParam, Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl

findValueByID.

Flexigrid - Class in net.sourceforge.solexatools.webapp.metamodel

Flexigrid class.

Flexigrid(int, int) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid

Constructor for Flexigrid.

Flexigrid(int) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid

Constructor for Flexigrid.

Flexigrid() - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid

Constructor for Flexigrid.

Flexigrid.Cells - Class in net.sourceforge.solexatools.webapp.metamodel

Flexigrid.Cells(List<String>) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells

Flexigrid.ColumnModel - Class in net.sourceforge.solexatools.webapp.metamodel

Flexigrid.ColumnModel(String, String, int, boolean, String) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel

flush() - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

FORCE_HOST - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

forJSON(String) - Static method in class net.sourceforge.seqware.common.util.jsontools.JsonUtil

forJSON.

forJSON(String) - Static method in class net.sourceforge.solexatools.util.ModelUtil

forJSON.

format(String, Object...) - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

format(Map<String, ? extends OptionDescriptor>) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.MarkDownFormatter

Freemarker - Class in net.sourceforge.seqware.common.util.freemarker

Freemarker class.

Freemarker() - Constructor for class net.sourceforge.seqware.common.util.freemarker.Freemarker

FREEMARKEREXCEPTION - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant FREEMARKEREXCEPTION=70

fromDto(AttributeDto, Class<T>) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos

fromDto.

fromWorkflow(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowReport

fromWorkflow.

G

GCR_STDERR - Static variable in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

GCR_STDERR_BUFFERSIZE - Static variable in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

GCR_STDOUT - Static variable in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

GCR_STDOUT_BUFFERSIZE - Static variable in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

generateDax(AbstractWorkflowDataModel, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.DaxgeneratorV2

generate a dax file from the object model

generateDaxFile(WorkflowInfo, File, String, Map<String, String>, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

generateDaxFile.

generatedValue(String) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools

generateLaneInfo(String, int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

Generates lane info with the given parameters.

generateRunInfo(String, String, String, String, String, String, String, String, String, int, int, boolean, String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

Generates a RunInfo object with the given parameters.

generateRunnerLine() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob

generateRunnerLine() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob

generateSampleInfo(String, String, String, String, String, String, String, String, String, int, String, String, String, String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

Generates a sample info object given the fields, and prompts for null fields if the interactive flag is on.

generateWorkflowXml(AbstractWorkflowDataModel, String, String, Path, boolean, File, String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowXmlGenerator

generate a dax file from the object model

GenericCommandRunner - Class in net.sourceforge.seqware.pipeline.modules

This is a very simple module that takes a few options on the command line and then passes the rest of the arguments to whatever command is specified.

GenericCommandRunner() - Constructor for class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

GenericDBResource - Class in net.sourceforge.seqware.webservice.resources.queries

GenericDBResource class.

GenericDBResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.GenericDBResource

Constructor for GenericDBResource.

GenericMetadataSaver - Class in net.sourceforge.seqware.pipeline.modules

Deprecated.

Deprecating this in favour of Metadata(plugin) and the new CLI

GenericMetadataSaver() - Constructor for class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver

Deprecated.

GEO_REACTION_ID_ATTR_TAG - Static variable in class net.sourceforge.seqware.common.model.Sample

The presence of this attribute is used to identify that the sample is a library

get(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService

get.

get(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl

get.

get(File) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO

get.

get(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO

get.

get(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate

get.

get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate

get.

get(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate

get.

get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate

get.

get(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate

get.

get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate

get.

get(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO

get.

get(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO

get.

get(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO

get.

get(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO

get.

get() - Static method in class net.sourceforge.seqware.common.factory.DBAccess

get(Map<String, String>) - Static method in class net.sourceforge.seqware.common.metadata.MetadataFactory

get() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter

get() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter

get() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource

get() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionResource

get() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource

get_description() - Method in class io.seqware.pipeline.plugins.sanity.SanityCheck

get_description.

get_description() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface

Generates a short description of the plugin, preferably one line.

get_description() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

Generates a short description of the plugin, preferably one line.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin

Generates a short description of the plugin, preferably one line.

get_description() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface

Generates a short description of the plugin, preferably one line.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator

Generates a short description of the plugin, preferably one line.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection

Generates a short description of the plugin, preferably one line.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager

get_description.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB

get_description.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker

Generates a short description of the plugin, preferably one line.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.deletion.DeletionDB

get_description.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.fileprovenance.FileProvenanceReporter

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld

get_description.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin

get_description.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

Generates a short description of the plugin, preferably one line.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner

get_description.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter

Generates a short description of the plugin, preferably one line.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter

Generates a short description of the plugin, preferably one line.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin

get_description.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter

Generates a short description of the plugin, preferably one line.

get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker

Generates a short description of the plugin, preferably one line.

get_galaxy_xml() - Method in class net.sourceforge.seqware.pipeline.module.Module

Output Galaxy definition files so you can use this module with Galaxy.

get_syntax() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface

Generates a "help" message for the user of the plugin.

get_syntax() - Method in class net.sourceforge.seqware.pipeline.module.Module

Generates a "help" message for the user of the module.

get_syntax() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface

Generates a "help" message for the user of the module.

get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

Generates a "help" message for the user of the module.

get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver

Deprecated.

Generates a "help" message for the user of the module.

get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle

get_syntax.

get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

get_syntax.

get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

get_syntax.

get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

get_syntax.

get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory

get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin

Generates a "help" message for the user of the plugin.

get_syntax() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface

Generates a "help" message for the user of the plugin.

get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld

Generates a "help" message for the user of the plugin.

get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin

Generates a "help" message for the user of the plugin.

get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin

Generates a "help" message for the user of the plugin.

get_workflow_info(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

get_workflow_info.

get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

get_workflow_info.

get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

get_workflow_info.

get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

get_workflow_info.

get_workflow_run_accession(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

get_workflow_run_accession.

get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

get_workflow_run_accession.

get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

get_workflow_run_accession.

get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

get_workflow_run_accession.

get_workflow_run_id(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

get_workflow_run_id.

get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

get_workflow_run_id.

get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

get_workflow_run_id.

get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

get_workflow_run_id.

getAbstract1() - Method in class io.seqware.webservice.generated.model.Study

getAbstractStr() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field abstractStr.

getAccession() - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple

getAccession() - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple

getAccession() - Method in class io.seqware.webservice.generated.model.Experiment

getAccession() - Method in class io.seqware.webservice.generated.model.Organism

getAccession() - Method in class io.seqware.webservice.generated.model.Study

getAccession() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field accession.

getAccession() - Method in class net.sourceforge.seqware.common.model.Organism

Getter for the field accession.

getAccession() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field accession.

getAccessionFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieBashJob

getAccessionFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieProvisionFileJob

getAccessionFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

getAccessionFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

getActive() - Method in class io.seqware.webservice.generated.model.ShareExperiment

getActive() - Method in class io.seqware.webservice.generated.model.ShareFile

getActive() - Method in class io.seqware.webservice.generated.model.ShareLane

getActive() - Method in class io.seqware.webservice.generated.model.ShareProcessing

getActive() - Method in class io.seqware.webservice.generated.model.ShareSample

getActive() - Method in class io.seqware.webservice.generated.model.ShareStudy

getActive() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

getActive() - Method in class net.sourceforge.seqware.common.model.ShareExperiment

Getter for the field active.

getActive() - Method in class net.sourceforge.seqware.common.model.ShareFile

Getter for the field active.

getActive() - Method in class net.sourceforge.seqware.common.model.ShareLane

Getter for the field active.

getActive() - Method in class net.sourceforge.seqware.common.model.ShareProcessing

Getter for the field active.

getActive() - Method in class net.sourceforge.seqware.common.model.ShareSample

Getter for the field active.

getActive() - Method in class net.sourceforge.seqware.common.model.ShareStudy

Getter for the field active.

getActive() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

Getter for the field active.

getAdapters() - Method in class io.seqware.webservice.generated.model.Sample

getAdapters() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field adapters.

getAdapterSpec() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

getAdapterSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Getter for the field adapterSpec.

getAddedSurcharge() - Method in class io.seqware.webservice.generated.model.Expense

getAddedSurcharge() - Method in class net.sourceforge.seqware.common.model.Expense

Getter for the field addedSurcharge.

getAdminModelClass() - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple

getAdminModelClass() - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple

getAgent() - Method in class io.seqware.webservice.generated.model.Expense

getAgent() - Method in class net.sourceforge.seqware.common.model.Expense

Getter for the field agent.

getAlgo() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

get the job algorithm

getAlgorithm() - Method in class io.seqware.webservice.generated.model.Processing

getAlgorithm() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field algorithm.

getAlgorithm() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field algorithm.

getAlgorithm() - Method in class net.sourceforge.seqware.pipeline.module.Module

Getter for the field algorithm.

getAlgorithm() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface

getAlgorithm.

getAlgorithm() - Method in class net.sourceforge.seqware.pipeline.module.TestModule

Getter for the field algorithm.

getAlias() - Method in class io.seqware.webservice.generated.model.Experiment

getAlias() - Method in class io.seqware.webservice.generated.model.Ius

getAlias() - Method in class io.seqware.webservice.generated.model.Lane

getAlias() - Method in class io.seqware.webservice.generated.model.Sample

getAlias() - Method in class io.seqware.webservice.generated.model.Study

getAlias() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field alias.

getAlias() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field alias.

getAlias() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field alias.

getAlias() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field alias.

getAlign() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel

getAll() - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO

getAll.

getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate

getAll.

getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate

getAll.

getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate

getAll.

getAll() - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO

getAll.

getAll() - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO

getAll.

getAllHtml(Lane, Registration, String, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil

getAllHtml.

getAllHtml(IUS, Registration, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil

getAllHtml.

getAllHtml(Processing, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil

getAllHtml.

getAllHtml(Processing, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil

getAllHtml.

getAllHtml(IUS, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil

getAllHtml.

getAllHtml(Study, Registration, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil

getAllHtml.

getAllHtml(Experiment, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil

getAllHtml.

getAllHtml(Sample, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil

getAllHtml.

getAllHtml(Lane, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil

getAllHtml.

getAllInputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Getter for the field allInputFiles.

getAllItems() - Method in class net.sourceforge.solexatools.util.PageInfo

Getter for the field allItems.

getAllProcessing() - Method in class net.sourceforge.seqware.common.model.SequencerRun

getAllProcessing.

getAllProcessings() - Method in class net.sourceforge.seqware.common.model.Lane

getAllProcessings.

getAllRuns() - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport

Find all of the workflow runs, and report on each of the workflow runs the files, samples and processing events associated with each.

getAllSelectedFiles(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

Get all selected Files, the files are organized by the name of the parameter (key) and a list of files selected (value) via a hash.

getAllSequencerRuns() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Get all of the sequencer runs in the DB.

getAllSequencerRuns() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getAllSequencerRuns() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getAllSequencerRuns() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getAllSequencerRuns.

getAllStudies() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getAllStudies.

getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getAllStudies.

getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getAllStudies.

getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getAllStudies.

getAnalysisWorkflowHtml(WorkflowRun, Registration, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil

getAnalysisWorkflowHtml.

getAncestorWorkflowRunId() - Method in class io.seqware.webservice.generated.model.Processing

getAnonymizedName() - Method in class io.seqware.webservice.generated.model.Sample

getAnonymizedName() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field anonymizedName.

getApplication() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource

getApplicationInfo(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication

getApplicationInfo(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion

getArch() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

getArguments() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command

getArguments() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule

Getter for the field arguments.

getAssayType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of assayType

getAsText() - Method in class net.sourceforge.solexatools.validation.CustomIntegerEditor

getAsText.

getAttribute(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue

getAttribute.

getAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource

Getter for the field attribute.

getAttribute() - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource

getAttribute.

getAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource

getAttribute.

getAttributes() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field attributes.

getAttributes() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Getter for the field attributes.

getAttributes() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto

Getter for the field attributes.

getBarcode() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Get the value of barcode

getBarcode() - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Getter for the field barcode.

getBaseCaller() - Method in class io.seqware.webservice.generated.model.Experiment

getBaseCaller() - Method in class io.seqware.webservice.generated.model.SequencerRun

getBaseCaller() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field baseCaller.

getBaseCoord() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

getBaseCoord() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Getter for the field baseCoord.

getBaseDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field baseDir.

getBaseIniFile() - Method in class io.seqware.webservice.generated.model.Workflow

getBaseIniFile() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field baseIniFile.

getBatchedJobsCount() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp.BucketGenerator

getBatchSize() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieBashJob

getBatchSize() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieProvisionFileJob

getBundle_version() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getBundleInfo(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

getBundleInfo.

getCell() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells

getCenterName() - Method in class io.seqware.webservice.generated.model.Experiment

getCenterName() - Method in class io.seqware.webservice.generated.model.Study

getCenterName() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field centerName.

getCenterName() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field centerName.

getCenterProjectName() - Method in class io.seqware.webservice.generated.model.Study

getCenterProjectName() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field centerProjectName.

getChildId() - Method in class io.seqware.webservice.generated.model.ProcessingRelationship

getChildId() - Method in class io.seqware.webservice.generated.model.SampleRelationship

getChildren() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field children.

getChildren() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field children.

getChildren() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

getChildren() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

getChildrenUrls() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Getter for the field childrenUrls.

getChildSample() - Method in class net.sourceforge.seqware.common.model.FileReportRow

Getter for the field childSample.

getChildSample() - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Getter for the field childSample.

getChildSample() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId

Getter for the field childSample.

getChildSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Getter for the field childSample.

getChildSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Getter for the field childSample.

getChildSampleId() - Method in class io.seqware.webservice.generated.model.FileReport

getChildSampleId() - Method in class io.seqware.webservice.generated.model.SampleReport

getChildSamples(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

getChildSamples.

getChildSamples(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

getChildSamples.

getChildSamples(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

getChildSamples.

getChildSamples(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

getChildSamples.

getChildSamplesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Get the child samples of a parent sample.

getChildSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getChildSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getChildSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getClassesDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field classesDir.

getClassPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

getClient() - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

getClientNotes() - Method in class io.seqware.webservice.generated.model.Invoice

getClientNotes() - Method in class net.sourceforge.seqware.common.model.Invoice

Getter for the field clientNotes.

getCmd() - Method in class io.seqware.webservice.generated.model.Workflow

getCmd() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getCode() - Method in class io.seqware.webservice.generated.model.LaneType

getCode() - Method in class io.seqware.webservice.generated.model.Organism

getCode() - Method in class net.sourceforge.seqware.common.model.Organism

Getter for the field code.

getCode() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto

Getter for the field code.

getColorMatrix() - Method in class io.seqware.webservice.generated.model.SequencerRun

getColorMatrix() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field colorMatrix.

getColorMatrix() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field colorMatrix.

getColorMatrixCode() - Method in class io.seqware.webservice.generated.model.SequencerRun

getColorMatrixCode() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field colorMatrixCode.

getColorMatrixCode() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field colorMatrixCode.

getCommand() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field command.

getCommand() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field command.

getCommand() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field command.

getCommand() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

getCommand() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

getCommand() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

getCommonName() - Method in class io.seqware.webservice.generated.model.Sample

getCompleted() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Getter for the field completed.

getCompute() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getComputeReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field computeReq.

getConfigPath() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field configPath.

getConfigs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getConfiguration() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication

Getter for the field configuration.

getConfiguration() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion

Getter for the field configuration.

getConfirmEmailAddress() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO

Getter for the field confirmEmailAddress.

getConfirmPassword() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO

Getter for the field confirmPassword.

getConstructionProtocol() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

getConstructionProtocol() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Getter for the field constructionProtocol.

getCountFile() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field countFile.

getCountFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

getCountFiles.

getCountFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

getCountFiles.

getCountFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

getCountFiles.

getCountFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

getCountFiles.

getCreated() - Method in class net.sourceforge.seqware.common.model.SampleSearch

Getter for the field created.

getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field createTimestamp.

getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Invoice

Getter for the field createTimestamp.

getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field createTimestamp.

getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field createTimestamp.

getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field createTimestamp.

getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Registration

Getter for the field createTimestamp.

getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field createTimestamp.

getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field createTimestamp.

getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field createTimestamp.

getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareStudy

Getter for the field createTimestamp.

getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

Getter for the field createTimestamp.

getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field createTimestamp.

getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field createTimestamp.

getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field createTimestamp.

getCreateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Getter for the field createTimeStamp.

getCreateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Getter for the field createTimeStamp.

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Experiment

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Invoice

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Ius

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Lane

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Processing

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Registration

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Sample

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.SampleSearch

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.SequencerRun

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareExperiment

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareFile

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareLane

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareProcessing

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareSample

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareStudy

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Study

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Workflow

getCreateTstmp() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareExperiment

Getter for the field createTstmp.

getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareFile

Getter for the field createTstmp.

getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareLane

Getter for the field createTstmp.

getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareProcessing

Getter for the field createTstmp.

getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareSample

Getter for the field createTstmp.

getCriteria() - Method in class net.sourceforge.solexatools.webapp.controller.SearchController

Getter for the field criteria.

getCurrentBucket() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp.BucketGenerator

getCurrentSelectedFiles(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

getCurrentSelectedFiles.

getCurrentSelectedNodes(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

getCurrentSelectedNodes.

getCurrentWorkflow(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

getCurrentWorkflow.

getCurrentWorkflowParam(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

getCurrentWorkflowParam.

getCurrentWorkingDir() - Method in class io.seqware.webservice.generated.model.Workflow

getCurrentWorkingDir() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getCurrentWorkingDir() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field currentWorkingDir.

getCwd() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field cwd.

getCycleCoord() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

getCycleCoord() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Getter for the field cycleCoord.

getCycleCount() - Method in class io.seqware.webservice.generated.model.Lane

getCycleCount() - Method in class io.seqware.webservice.generated.model.SequencerRun

getCycleCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field cycleCount.

getCycleCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field cycleCount.

getCycleDescriptor() - Method in class io.seqware.webservice.generated.model.Lane

getCycleDescriptor() - Method in class io.seqware.webservice.generated.model.SequencerRun

getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field cycleDescriptor.

getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field cycleDescriptor.

getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field cycleDescriptor.

getCycles() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field cycles.

getCycles() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field cycles.

getCycleSequence() - Method in class io.seqware.webservice.generated.model.Lane

getCycleSequence() - Method in class io.seqware.webservice.generated.model.SequencerRun

getCycleSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field cycleSequence.

getCycleSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field cycleSequence.

getDate() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

getDate() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getDax() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getDax() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field dax.

getDaxDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getDaysUntilDue() - Method in class io.seqware.webservice.generated.model.Invoice

getDaysUntilDue() - Method in class net.sourceforge.seqware.common.model.Invoice

Getter for the field daysUntilDue.

getDb() - Method in class io.seqware.webservice.generated.model.ExperimentLink

getDb() - Method in class io.seqware.webservice.generated.model.IusLink

getDb() - Method in class io.seqware.webservice.generated.model.LaneLink

getDb() - Method in class io.seqware.webservice.generated.model.SampleLink

getDb() - Method in class io.seqware.webservice.generated.model.StudyLink

getDb() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

Getter for the field db.

getDB(Map<String, String>) - Static method in class net.sourceforge.seqware.common.metadata.MetadataFactory

getDb() - Method in class net.sourceforge.seqware.common.model.ExperimentLink

Getter for the field db.

getDb() - Method in class net.sourceforge.seqware.common.model.IUSLink

Getter for the field db.

getDb() - Method in class net.sourceforge.seqware.common.model.LaneLink

Getter for the field db.

getDb() - Method in class net.sourceforge.seqware.common.model.SampleLink

Getter for the field db.

getDb() - Method in class net.sourceforge.seqware.common.model.StudyLink

Getter for the field db.

getDbmd() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

Getter for the field dbmd.

getDecodeMethod() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

getDecodeMethod() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Getter for the field decodeMethod.

getDecryptCipher(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Gets cipher by DecryptKey.

getDecryptCipher() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

getDecryptCipher.

getDEFAULT_DB_HOST() - Method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator

getDEFAULT_DB_HOST() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

getDEFAULT_DB_HOST() - Method in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator

getDefaultDirManagerExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils

getDefaultJavaExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils

getDefaultJavaLocalExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils

getDefaultPerlExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils

getDefaultValue() - Method in class io.seqware.webservice.generated.model.WorkflowParam

getDefaultValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Getter for the field defaultValue.

getDependentElement(PegasusJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.BundleDir_Check

getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.CLICheck

getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_Check

getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_WS_ConsistencyCheck

getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.HDFS_Check

getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.Oozie_Check

getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.Script_Check

getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.TutorialCheck

getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.WS_Check

getDescription() - Method in interface io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface

Describes the check and indicates what may be wrong

getDescription() - Method in class io.seqware.webservice.generated.model.Expense

getDescription() - Method in class io.seqware.webservice.generated.model.Experiment

getDescription() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

getDescription() - Method in class io.seqware.webservice.generated.model.File

getDescription() - Method in class io.seqware.webservice.generated.model.Ius

getDescription() - Method in class io.seqware.webservice.generated.model.Lane

getDescription() - Method in class io.seqware.webservice.generated.model.LibrarySelection

getDescription() - Method in class io.seqware.webservice.generated.model.LibrarySource

getDescription() - Method in class io.seqware.webservice.generated.model.LibraryStrategy

getDescription() - Method in class io.seqware.webservice.generated.model.Platform

getDescription() - Method in class io.seqware.webservice.generated.model.Processing

getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingIus

getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingLanes

getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingSamples

getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingStudies

getDescription() - Method in class io.seqware.webservice.generated.model.Sample

getDescription() - Method in class io.seqware.webservice.generated.model.SequencerRun

getDescription() - Method in class io.seqware.webservice.generated.model.Study

getDescription() - Method in class io.seqware.webservice.generated.model.StudyType

getDescription() - Method in class io.seqware.webservice.generated.model.Workflow

getDescription() - Method in class net.sourceforge.seqware.common.model.Expense

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.LibrarySelection

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.LibrarySource

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.Platform

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingIus

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.StudyType

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.module.FileMetadata

getDescription() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.webservice.dto.FileDto

Getter for the field description.

getDescription() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Getter for the field description.

getDeveloperMl() - Method in class io.seqware.webservice.generated.model.Registration

getDirContext() - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication

getDirContext.

getDirectories() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getDirectoriesNumber() - Method in class net.sourceforge.solexatools.util.FileFinder

Getter for the field directoriesNumber.

getDirectorySize() - Method in class net.sourceforge.solexatools.util.FileFinder

getDirectorySize.

getDisplay() - Method in class io.seqware.webservice.generated.model.WorkflowParam

getDisplay() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Getter for the field display.

getDisplay() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel

getDisplayName() - Method in class io.seqware.webservice.generated.model.FileType

getDisplayName() - Method in class io.seqware.webservice.generated.model.WorkflowParam

getDisplayName() - Method in class io.seqware.webservice.generated.model.WorkflowParamValue

getDisplayName() - Method in class net.sourceforge.seqware.common.model.FileType

Getter for the field displayName.

getDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Getter for the field displayName.

getDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

Getter for the field displayName.

getDisplayName() - Method in class net.sourceforge.solexatools.util.SummaryLine

Getter for the field displayName.

getDisplayValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Getter for the field displayValue.

getDomainObject() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO

Getter for the field domainObject.

getDomainObject() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO

Getter for the field domainObject.

getEmail() - Method in class io.seqware.webservice.generated.model.Registration

getEmail() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto

Getter for the field email.

getEmailAddress() - Method in class net.sourceforge.seqware.common.model.Registration

Getter for the field emailAddress.

getEncryptCipher(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Gets cipher by EncryptKey.

getEncryptCipher() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

getEncryptCipher.

getEnd() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field end.

getEndDate() - Method in class io.seqware.webservice.generated.model.Invoice

getEndDate() - Method in class net.sourceforge.seqware.common.model.Invoice

Getter for the field endDate.

getEndPage() - Method in class net.sourceforge.solexatools.util.PageInfo

Getter for the field endPage.

getEntityManager() - Method in class io.seqware.webservice.generated.controller.AbstractFacade

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExpenseAttributeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExpenseFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentAttributeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentLibraryDesignFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentLinkFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignReadSpecFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.FileAttributeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.FileFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.FileReportFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.FileTypeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.InvoiceAttributeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.InvoiceFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.IusAttributeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.IusFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.IusLinkFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.IusWorkflowRunsFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.LaneAttributeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.LaneFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.LaneLinkFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.LaneTypeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.LaneWorkflowRunsFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.LibrarySelectionFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.LibrarySourceFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.LibraryStrategyFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.OrganismFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.PlatformFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingAttributeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingExperimentsFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingFilesFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingIusFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingLanesFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingRelationshipFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingSamplesFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingSequencerRunsFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingStudiesFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.RegistrationFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleAttributeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleLinkFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleRelationshipFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleReportFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleSearchAttributeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleSearchFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.SequencerRunAttributeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.SequencerRunFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareExperimentFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareFileFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareLaneFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareProcessingFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareSampleFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareStudyFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareWorkflowRunFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.StudyAttributeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.StudyFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.StudyLinkFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.StudyTypeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowAttributeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowParamFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowParamValueFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowRunAttributeFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowRunFacadeREST

getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowRunParamFacadeREST

getEntityUrl() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto

Getter for the field entityUrl.

getEnv() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getError() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread

Getter for the field error.

getErrorCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

getErrorCnt.

getErrorCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

Deprecated.

getErrorCnt() - Method in class net.sourceforge.seqware.common.model.Lane

getErrorCnt.

getErrorCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun

getErrorCnt.

getErrorCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

getErrorCnt.

getErrorCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field errorCount.

getExecutionEnv() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getExistingType() - Method in class io.seqware.webservice.generated.model.Study

getExistingType() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field existingType.

getExistingTypeInt() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field existingTypeInt.

getExitCode() - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException

getExitCode.

getExitCode() - Method in exception net.sourceforge.seqware.common.err.SeqwareException

getExitCode.

getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwBadFileException

getExitCode.

getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwBadModuleException

getExitCode.

getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwParameterException

getExitCode.

getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwRunnerParameterException

getExitCode.

getExitStatus() - Method in class io.seqware.webservice.generated.model.Processing

getExitStatus() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field exitStatus.

getExitStatus() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field exitStatus.

getExpectedBasecall() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

getExpectedBaseCall() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Getter for the field expectedBaseCall.

getExpectedNumberReads() - Method in class io.seqware.webservice.generated.model.Experiment

getExpectedNumberReads() - Method in class io.seqware.webservice.generated.model.Sample

getExpectedNumberReads() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field expectedNumberReads.

getExpectedNumberRuns() - Method in class io.seqware.webservice.generated.model.Experiment

getExpectedNumberRuns() - Method in class io.seqware.webservice.generated.model.Sample

getExpectedNumberRuns() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field expectedNumberRuns.

getExpectedNumberSpots() - Method in class io.seqware.webservice.generated.model.Experiment

getExpectedNumberSpots() - Method in class io.seqware.webservice.generated.model.Sample

getExpectedNumberSpots() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field expectedNumberSpots.

getExpectedNumReads() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field expectedNumReads.

getExpectedNumRuns() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field expectedNumRuns.

getExpectedNumSpots() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field expectedNumSpots.

getExpenseAttributeCollection() - Method in class io.seqware.webservice.generated.model.Expense

getExpenseAttributeId() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute

getExpenseCollection() - Method in class io.seqware.webservice.generated.model.Invoice

getExpenseFinishedTstmp() - Method in class io.seqware.webservice.generated.model.Expense

getExpenseId() - Method in class io.seqware.webservice.generated.model.Expense

getExpenseId() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute

getExpenseId() - Method in class net.sourceforge.seqware.common.model.Expense

Getter for the field expenseId.

getExpenses() - Method in class net.sourceforge.seqware.common.model.Invoice

Getter for the field expenses.

getExpenseType() - Method in class io.seqware.webservice.generated.model.Expense

getExpenseType() - Method in class net.sourceforge.seqware.common.model.Expense

Getter for the field expenseType.

getExperiment(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getExperiment.

getExperiment(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getExperiment(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getExperiment(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getExperiment() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

Getter for the field experiment.

getExperiment() - Method in class net.sourceforge.seqware.common.model.ExperimentLink

Getter for the field experiment.

getExperiment() - Method in class net.sourceforge.seqware.common.model.FileReportRow

Getter for the field experiment.

getExperiment() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments

Getter for the field experiment.

getExperiment() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field experiment.

getExperiment() - Method in class net.sourceforge.seqware.common.model.ShareExperiment

Getter for the field experiment.

getExperimentAttributeCollection() - Method in class io.seqware.webservice.generated.model.Experiment

getExperimentAttributeId() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute

getExperimentAttributeId() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

Getter for the field experimentAttributeId.

getExperimentAttributes() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field experimentAttributes.

getExperimentAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of experimentAttributes

getExperimentCollection() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

getExperimentCollection() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

getExperimentCollection() - Method in class io.seqware.webservice.generated.model.Platform

getExperimentCollection() - Method in class io.seqware.webservice.generated.model.Registration

getExperimentCollection() - Method in class io.seqware.webservice.generated.model.Study

getExperimentDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of experimentDescription

getExperimentHtml(Experiment, Registration, String, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil

getExperimentHtml.

getExperimentId() - Method in class io.seqware.webservice.generated.model.Experiment

getExperimentId() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute

getExperimentId() - Method in class io.seqware.webservice.generated.model.ExperimentLink

getExperimentId() - Method in class io.seqware.webservice.generated.model.FileReport

getExperimentId() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

getExperimentId() - Method in class io.seqware.webservice.generated.model.Sample

getExperimentId() - Method in class io.seqware.webservice.generated.model.ShareExperiment

getExperimentId() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field experimentId.

getExperimentLibraryDesign() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field experimentLibraryDesign.

getExperimentLibraryDesignCollection() - Method in class io.seqware.webservice.generated.model.LibrarySelection

getExperimentLibraryDesignCollection() - Method in class io.seqware.webservice.generated.model.LibrarySource

getExperimentLibraryDesignCollection() - Method in class io.seqware.webservice.generated.model.LibraryStrategy

getExperimentLibraryDesignId() - Method in class io.seqware.webservice.generated.model.Experiment

getExperimentLibraryDesignId() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

getExperimentLibraryDesignId() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Getter for the field experimentLibraryDesignId.

getExperimentLibraryDesigns() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getExperimentLibraryDesigns.

getExperimentLibraryDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getExperimentLibraryDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getExperimentLibraryDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getExperimentLibraryDesignService() - Method in class net.sourceforge.seqware.common.ContextImpl

getExperimentLibraryDesignService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Getter for the field experimentLibraryDesignService.

getExperimentLibraryDesignServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getExperimentLinkCollection() - Method in class io.seqware.webservice.generated.model.Experiment

getExperimentLinkId() - Method in class io.seqware.webservice.generated.model.ExperimentLink

getExperimentLinkId() - Method in class net.sourceforge.seqware.common.model.ExperimentLink

Getter for the field experimentLinkId.

getExperimentLinks() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field experimentLinks.

getExperimentName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of experimentName

getExperiments() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field experiments.

getExperiments() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field experiments.

getExperimentService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field experimentService.

getExperimentService() - Method in class net.sourceforge.solexatools.validation.ExperimentValidator

Getter for the field experimentService.

getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Getter for the field experimentService.

getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Getter for the field experimentService.

getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Getter for the field experimentService.

getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController

Getter for the field experimentService.

getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Getter for the field experimentService.

getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController

Getter for the field experimentService.

getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController

Getter for the field experimentService.

getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController

Getter for the field experimentService.

getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Getter for the field experimentService.

getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

Getter for the field experimentService.

getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

Getter for the field experimentService.

getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Getter for the field experimentService.

getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Getter for the field experimentService.

getExperimentServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getExperimentServiceBean.

getExperimentsFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Get experiments from a study.

getExperimentsFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getExperimentsFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getExperimentsFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getExperimentSpotDesign() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field experimentSpotDesign.

getExperimentSpotDesign() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Getter for the field experimentSpotDesign.

getExperimentSpotDesignId() - Method in class io.seqware.webservice.generated.model.Experiment

getExperimentSpotDesignId() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

getExperimentSpotDesignId() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

getExperimentSpotDesignId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Getter for the field experimentSpotDesignId.

getExperimentSpotDesignReadSpecCollection() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

getExperimentSpotDesignReadSpecId() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

getExperimentSpotDesignReadSpecId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Getter for the field experimentSpotDesignReadSpecId.

getExperimentSpotDesignReadSpecs() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getPlatforms.

getExperimentSpotDesignReadSpecs() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getExperimentSpotDesignReadSpecs() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getExperimentSpotDesignReadSpecs() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getExperimentSpotDesignReadSpecService() - Method in class net.sourceforge.seqware.common.ContextImpl

getExperimentSpotDesignReadSpecService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Getter for the field experimentSpotDesignReadSpecService.

getExperimentSpotDesignReadSpecServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getExperimentSpotDesigns() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getExperimentSpotDesigns.

getExperimentSpotDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getExperimentSpotDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getExperimentSpotDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getExperimentSpotDesignService() - Method in class net.sourceforge.seqware.common.ContextImpl

getExperimentSpotDesignService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Getter for the field experimentSpotDesignService.

getExperimentSpotDesignServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getExperimentSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

getExpLibDesignDesc() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field expLibDesignDesc.

getExpLibDesignName() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field expLibDesignName.

getExpLibDesignProtocol() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field expLibDesignProtocol.

getExpLibDesignSelection() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field expLibDesignSelection.

getExpLibDesignSource() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field expLibDesignSource.

getExpLibDesignStrategy() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field expLibDesignStrategy.

getExpSpotDesignAdapterSpec() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field expSpotDesignAdapterSpec.

getExpSpotDesignReadsPerSpot() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field expSpotDesignReadsPerSpot.

getExpSpotDesignTagSpec() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field expSpotDesignTagSpec.

getExtension() - Method in class io.seqware.webservice.generated.model.FileType

getExtension() - Method in class net.sourceforge.seqware.common.model.FileType

Getter for the field extension.

getExtension(String) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator

getExtension.

getExternalId() - Method in class io.seqware.webservice.generated.model.Invoice

getExternalId() - Method in class net.sourceforge.seqware.common.model.Invoice

Getter for the field externalId.

getFailed() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Getter for the field failed.

getFailedCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

getFailedCount.

getFailedCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService

getFailedCount.

getFailedJobsInfo(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools

This method will examine a Pegasus DAX log directory for a given workflow and identify the log files for jobs that failed.

getFile() - Method in class net.sourceforge.seqware.common.business.UploadFile

Getter for the field file.

getFile(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getFile.

getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getFile.

getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getFile.

getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getFile.

getFile() - Method in class net.sourceforge.seqware.common.model.FileAttribute

Getter for the field file.

getFile() - Method in class net.sourceforge.seqware.common.model.FileReportRow

Getter for the field file.

getFile() - Method in class net.sourceforge.seqware.common.model.ShareFile

Getter for the field file.

getFile() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Getter for the field file.

getFileAttributeCollection() - Method in class io.seqware.webservice.generated.model.File

getFileAttributeId() - Method in class io.seqware.webservice.generated.model.FileAttribute

getFileAttributeId() - Method in class net.sourceforge.seqware.common.model.FileAttribute

Getter for the field fileAttributeId.

getFileAttributes(Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService

Returns a complete set of attributes for a give File.

getFileAttributes(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl

Returns a complete set of attributes for a give File.

getFileAttributes() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field fileAttributes.

getFileAttributes() - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributesResource

getFileAttributes.

getFileAttributes() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributesServerResource

getFileAttributes.

getFileAttributeService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field fileAttributeService.

getFileAttributeServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getFileAttributeServiceBean.

getFileCollection() - Method in class io.seqware.webservice.generated.model.FileType

getFileCollection() - Method in class io.seqware.webservice.generated.model.Registration

getFileCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getFileHtml(Processing, Registration) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil

getFileHtml.

getFileHtml(Processing, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil

getFileHtml.

getFileHtml(Processing, WorkflowRun, Registration, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil

getFileHtml.

getFileId() - Method in class io.seqware.webservice.generated.model.File

getFileId() - Method in class io.seqware.webservice.generated.model.FileAttribute

getFileId() - Method in class io.seqware.webservice.generated.model.FileReport

getFileId() - Method in class io.seqware.webservice.generated.model.ProcessingFiles

getFileId() - Method in class io.seqware.webservice.generated.model.ShareFile

getFileId() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field fileId.

getFileMetaType() - Method in class io.seqware.webservice.generated.model.WorkflowParam

getFileMetaType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Getter for the field fileMetaType.

getFileMetaType() - Method in class net.sourceforge.solexatools.util.SummaryLine

Getter for the field fileMetaType.

getFilename() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

getFileName() - Method in class net.sourceforge.seqware.common.model.File

getFileName.

getFilename(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

getFileName() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Gets the file name.

getFilename() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

getFileName(String) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController

getFileName.

getFileOne() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field fileOne.

getFilePath() - Method in class io.seqware.webservice.generated.model.File

getFilePath() - Method in class io.seqware.webservice.generated.model.SequencerRun

getFilePath() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field filePath.

getFilePath() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field filePath.

getFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field filePath.

getFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field filePath.

getFilePath() - Method in class net.sourceforge.seqware.common.module.FileMetadata

getFilePath(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

getFilePath(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB

getFilePath.

getFilePath() - Method in class net.sourceforge.seqware.webservice.dto.FileDto

Getter for the field filePath.

getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

getFiles.

getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

getFiles.

getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService

getFiles.

getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.FileService

getFiles.

getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

getFiles.

getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

getFiles.

getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

getFiles.

getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

getFiles.

getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

getFiles.

getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

getFiles.

getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

getFiles.

getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

getFiles.

getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

getFiles.

getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

getFiles.

getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

getFiles.

getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

getFiles.

getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

getFiles.

getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

getFiles.

getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

getFiles.

getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService

getFiles.

getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.IUSService

getFiles.

getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService

getFiles.

getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.LaneService

getFiles.

getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

getFiles.

getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

getFiles.

getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService

getFiles.

getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.SampleService

getFiles.

getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService

getFiles.

getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.StudyService

getFiles.

getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

getFiles.

getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

getFiles.

getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

getFiles.

getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

getFiles.

getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

getFiles.

getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

getFiles.

getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

getFiles.

getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

getFiles.

getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

getFiles.

getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

getFiles.

getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

getFiles.

getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

getFiles.

getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

getFiles.

getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

getFiles.

getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

getFiles.

getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

getFiles.

getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

getFiles.

getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

getFiles.

getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

getFiles.

getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

getFiles.

getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

getFiles.

getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

getFiles.

getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

getFiles.

getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

getFiles.

getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

getFiles.

getFiles() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field files.

getFiles() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Getter for the field files.

getFiles() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field files.

getFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

getFiles(HttpServletRequest, String) - Static method in class net.sourceforge.solexatools.util.BulkUtil

getFiles.

getFiles() - Method in class net.sourceforge.solexatools.util.SummaryLine

Getter for the field files.

getFiles_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Getter for the field files_url.

getFilesArray() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

Getter for the field filesArray.

getFileService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field fileService.

getFileService() - Method in class net.sourceforge.solexatools.validation.UploadFileValidator

Getter for the field fileService.

getFileService() - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator

Getter for the field fileService.

getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController

Getter for the field fileService.

getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Getter for the field fileService.

getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController

Getter for the field fileService.

getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Getter for the field fileService.

getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.FileController

Getter for the field fileService.

getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController

Getter for the field fileService.

getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Getter for the field fileService.

getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController

Getter for the field fileService.

getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController

Getter for the field fileService.

getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Getter for the field fileService.

getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Getter for the field fileService.

getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Getter for the field fileService.

getFileServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getFileServiceBean.

getFileSize(String) - Static method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

getFileSize.

getFilesNumber() - Method in class net.sourceforge.solexatools.util.FileFinder

Getter for the field filesNumber.

getFileStatus() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

getFileSwa() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

getFileTwo() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field fileTwo.

getFileTwoURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field fileTwoURL.

getFileType() - Method in class net.sourceforge.seqware.common.business.UploadFile

Getter for the field fileType.

getFileType() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field fileType.

getFileType() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field fileType.

getFileTypeId() - Method in class io.seqware.webservice.generated.model.File

getFileTypeId() - Method in class io.seqware.webservice.generated.model.FileType

getFileTypeId() - Method in class net.sourceforge.seqware.common.business.UploadFile

Getter for the field fileTypeId.

getFileTypeId() - Method in class net.sourceforge.seqware.common.model.FileType

Getter for the field fileTypeId.

getFileTypeId() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field fileTypeId.

getFileTypeService() - Method in class net.sourceforge.solexatools.validation.UploadFileValidator

Getter for the field fileTypeService.

getFileTypeService() - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator

Getter for the field fileTypeService.

getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Getter for the field fileTypeService.

getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Getter for the field fileTypeService.

getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Getter for the field fileTypeService.

getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController

Getter for the field fileTypeService.

getFileUploadService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Getter for the field fileUploadService.

getFileURL() - Method in class net.sourceforge.seqware.common.business.UploadFile

Getter for the field fileURL.

getFileURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field fileURL.

getFileValidationServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getFileValidationServiceBean.

getFinalized() - Method in class io.seqware.webservice.generated.model.Invoice

getFinishedCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

getFinishedCount.

getFinishedCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService

getFinishedCount.

getFinishedTimestamp() - Method in class net.sourceforge.seqware.common.model.Expense

Getter for the field finishedTimestamp.

getFirstId(String) - Static method in class net.sourceforge.solexatools.util.Constant

getFirstId.

getFirstName() - Method in class io.seqware.webservice.generated.model.Registration

getFirstName() - Method in class net.sourceforge.seqware.common.model.Registration

Getter for the field firstName.

getFirstName() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto

Getter for the field firstName.

getFlowCount() - Method in class io.seqware.webservice.generated.model.SequencerRun

getFlowCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field flowCount.

getFlowCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field flowCount.

getFlowSequence() - Method in class io.seqware.webservice.generated.model.SequencerRun

getFlowSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field flowSequence.

getFlowSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field flowSequence.

getFolderStore() - Method in class net.sourceforge.seqware.common.business.UploadFile

Getter for the field folderStore.

getFolderStore() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field folderStore.

getForceRunAll() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

getFs_default_name() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getFs_defaultFS() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getFs_hdfs_impl() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getFullName() - Method in class net.sourceforge.seqware.common.model.Workflow

getFullName.

getFullyPaid() - Method in class io.seqware.webservice.generated.model.Invoice

getGcrOutputFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command

getGroupingStrategy() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

getHbase_master() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getHbase_zookeeper_property_clientPort() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getHbase_zookeeper_quorum() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getHeader() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

Deprecated.

getHeader() - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource

getHeader.

getHost() - Method in class io.seqware.webservice.generated.model.Workflow

getHost() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getHost() - Method in class net.sourceforge.seqware.common.model.Workflow

Deprecated.

getHost() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field host.

getHost() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field host.

getHtml() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field html.

getHtml() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field html.

getHtml() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field html.

getHtml(Object, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil

getHtml.

getHtml(Object, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil

getHtml.

getHtml(Object, Registration, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil

getHtml.

getHtml(WorkflowRun, Registration, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil

getHtml.

getHtml(Sample, WorkflowRun, Registration, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil

getHtml.

getHtml(Processing, WorkflowRun, Registration, String, List<String>, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil

getHtml.

getHttpInputStream(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

getHttpInputStream.

getId() - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple

getId() - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple

getId() - Method in class io.seqware.webservice.generated.model.ExperimentLink

getId() - Method in class io.seqware.webservice.generated.model.IusLink

getId() - Method in class io.seqware.webservice.generated.model.LaneLink

getId() - Method in class io.seqware.webservice.generated.model.SampleLink

getId() - Method in class io.seqware.webservice.generated.model.StudyLink

getId() - Method in class net.sourceforge.seqware.common.business.UploadFile

Getter for the field id.

getId() - Method in class net.sourceforge.seqware.common.model.ExperimentLink

Getter for the field id.

getId() - Method in class net.sourceforge.seqware.common.model.IUSLink

Getter for the field id.

getId() - Method in class net.sourceforge.seqware.common.model.LaneLink

Getter for the field id.

getId() - Method in class net.sourceforge.seqware.common.model.SampleLink

Getter for the field id.

getId() - Method in class net.sourceforge.seqware.common.model.StudyLink

Getter for the field id.

getId() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

get the job id

getId() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource

Getter for the field id.

getId(String) - Static method in class net.sourceforge.solexatools.util.Constant

getId.

getIdentitySamples() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Getter for the field identitySamples.

getIdsSelectedLane(HttpServletRequest, WorkflowParam) - Method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

getIdsSelectedLane.

getImmediateInputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Getter for the field immediateInputFiles.

getIndividualName() - Method in class io.seqware.webservice.generated.model.Sample

getIndividualName() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field individualName.

getIndividualNumber() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

getInfo() - Method in class net.sourceforge.seqware.common.model.FileType

getInfo.

getInfo() - Method in class net.sourceforge.solexatools.util.PageInfo

Getter for the field info.

getIniFile() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getIniFile() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field iniFile.

getInputAlgorithm() - Method in class io.seqware.webservice.generated.model.Workflow

getInputAlgorithm() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field inputAlgorithm.

getInputFileAccessions() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

getInstance() - Static method in class net.sourceforge.seqware.common.ContextImpl

getInstance.

getInstance() - Static method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

getInstitution() - Method in class io.seqware.webservice.generated.model.Registration

getInstitution() - Method in class net.sourceforge.seqware.common.model.Registration

Getter for the field institution.

getInstitution() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto

Getter for the field institution.

getInstrumentModel() - Method in class io.seqware.webservice.generated.model.Platform

getInstrumentModel() - Method in class net.sourceforge.seqware.common.model.Platform

Getter for the field instrumentModel.

getInstrumentName() - Method in class io.seqware.webservice.generated.model.SequencerRun

getInstrumentName() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field instrumentName.

getInstrumentName() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field instrumentName.

getInvitationCode() - Method in class io.seqware.webservice.generated.model.Registration

getInvitationCode() - Method in class net.sourceforge.seqware.common.model.Registration

Getter for the field invitationCode.

getInvoice() - Method in class net.sourceforge.seqware.common.model.Expense

Getter for the field invoice.

getInvoiceAttributeCollection() - Method in class io.seqware.webservice.generated.model.Invoice

getInvoiceAttributeId() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute

getInvoiceCollection() - Method in class io.seqware.webservice.generated.model.Registration

getInvoiceId() - Method in class io.seqware.webservice.generated.model.Expense

getInvoiceId() - Method in class io.seqware.webservice.generated.model.Invoice

getInvoiceId() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute

getInvoiceId() - Method in class net.sourceforge.seqware.common.model.Invoice

Getter for the field invoiceId.

getInvoiceService() - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController

Getter for the field invoiceService.

getInvoiceService() - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController

Getter for the field invoiceService.

getIsEnd() - Method in class net.sourceforge.solexatools.util.PageInfo

Getter for the field isEnd.

getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field isHasFile.

getIsHasFile() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field isHasFile.

getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field isHasFile.

getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field isHasFile.

getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field isHasFile.

getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field isHasFile.

getIsHasFile() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field isHasFile.

getIsInvitationCode() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams

Getter for the field isInvitationCode.

getIsPublic() - Method in class io.seqware.webservice.generated.model.Sample

getIsSelected() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field isSelected.

getIsSelected() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field isSelected.

getIsSelected() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field isSelected.

getIsSelected() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field isSelected.

getIsSelected() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field isSelected.

getIsSelected() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field isSelected.

getIsSelected() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field isSelected.

getIsSelected() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field isSelected.

getIsStart() - Method in class net.sourceforge.solexatools.util.PageInfo

Getter for the field isStart.

getIus() - Method in class net.sourceforge.seqware.common.model.FileReportRow

Getter for the field ius.

getIus() - Method in class net.sourceforge.seqware.common.model.IUSAttribute

Getter for the field ius.

getIus() - Method in class net.sourceforge.seqware.common.model.IUSLink

Getter for the field ius.

getIus() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field ius.

getIUS() - Method in class net.sourceforge.seqware.common.model.Lane

getIUS.

getIUS() - Method in class net.sourceforge.seqware.common.model.Processing

getIUS.

getIus() - Method in class net.sourceforge.seqware.common.model.ProcessingIus

Getter for the field ius.

getIUS() - Method in class net.sourceforge.seqware.common.model.Sample

getIUS.

getIus() - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Getter for the field ius.

getIus() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId

Getter for the field ius.

getIus() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field ius.

getIus() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem

Getter for the field ius.

getIus() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Getter for the field ius.

getIusAttributeCollection() - Method in class io.seqware.webservice.generated.model.Ius

getIusAttributeId() - Method in class io.seqware.webservice.generated.model.IusAttribute

getIusAttributeId() - Method in class net.sourceforge.seqware.common.model.IUSAttribute

Getter for the field iusAttributeId.

getIusAttributes() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field iusAttributes.

getIusAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Get the value of iusAttributes

getIusCollection() - Method in class io.seqware.webservice.generated.model.Lane

getIusCollection() - Method in class io.seqware.webservice.generated.model.Registration

getIusCollection() - Method in class io.seqware.webservice.generated.model.Sample

getIusDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Get the value of iusDescription

getIusFiles() - Method in interface net.sourceforge.seqware.webservice.resources.tables.IusFilesResource

List files associated with Ius.

getIusFiles() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusFilesServerResource

List files associated with Ius.

getIUSFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Get IUSes (barcodes) from a lane or sample.

getIUSFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getIUSFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getIUSFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getIUSHtml(IUS, Registration, String, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil

getIUSHtml.

getIusId() - Method in class io.seqware.webservice.generated.model.FileReport

getIusId() - Method in class io.seqware.webservice.generated.model.Ius

getIusId() - Method in class io.seqware.webservice.generated.model.IusAttribute

getIusId() - Method in class io.seqware.webservice.generated.model.IusLink

getIusId() - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns

getIusId() - Method in class io.seqware.webservice.generated.model.ProcessingIus

getIusId() - Method in class io.seqware.webservice.generated.model.SampleReport

getIusId() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field iusId.

getIusLinkCollection() - Method in class io.seqware.webservice.generated.model.Ius

getIusLinkId() - Method in class io.seqware.webservice.generated.model.IusLink

getIusLinkId() - Method in class net.sourceforge.seqware.common.model.IUSLink

Getter for the field iusLinkId.

getIusLinks() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field iusLinks.

getIusName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Get the value of iusName

getIusService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field iusService.

getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Getter for the field iusService.

getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

getIUSService.

getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSController

Getter for the field iusService.

getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSController

getIUSService.

getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController

Getter for the field iusService.

getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController

Getter for the field iusService.

getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController

getIUSService.

getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Getter for the field iusService.

getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

getIUSService.

getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Getter for the field iusService.

getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

getIUSService.

getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController

Getter for the field iusService.

getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController

getIUSService.

getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

Getter for the field iusService.

getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

getIUSService.

getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

getIUSService.

getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Getter for the field iusService.

getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

getIUSService.

getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Getter for the field iusService.

getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

getIUSService.

getIUSServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getIUSServiceBean.

getIusSkip() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Get the value of iusSkip

getIusSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

getIusSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

getIusTag() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

getIusWorkflowRunsCollection() - Method in class io.seqware.webservice.generated.model.Ius

getIusWorkflowRunsCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getIusWorkflowRunsId() - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns

getJobList() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

getJobObject() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

getJobObject() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

getJobs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow

get all jobs in current workflow

getJobScript() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob

getJoinDevelopersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration

Getter for the field joinDevelopersMailingList.

getJoinUsersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration

Getter for the field joinUsersMailingList.

getJson(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileChildLimitedWorkflowRunsResource

getJsonEscapeAlgorithm() - Method in class net.sourceforge.seqware.common.model.Processing

getJsonEscapeAlgorithm.

getJsonEscapeDefaultValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

getJsonEscapeDefaultValue.

getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Experiment

getJsonEscapeDescription.

getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.File

getJsonEscapeDescription.

getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.IUS

getJsonEscapeDescription.

getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Lane

getJsonEscapeDescription.

getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Processing

getJsonEscapeDescription.

getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Sample

getJsonEscapeDescription.

getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRun

getJsonEscapeDescription.

getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Study

getJsonEscapeDescription.

getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Workflow

getJsonEscapeDescription.

getJsonEscapeDescription200() - Method in class net.sourceforge.seqware.common.model.Experiment

getJsonEscapeDescription200.

getJsonEscapeDescription200() - Method in class net.sourceforge.seqware.common.model.Study

getJsonEscapeDescription200.

getJsonEscapeDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

getJsonEscapeDisplayName.

getJsonEscapeDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

getJsonEscapeDisplayName.

getJsonEscapeFileName() - Method in class net.sourceforge.seqware.common.model.File

getJsonEscapeFileName.

getJsonEscapeFullName() - Method in class net.sourceforge.seqware.common.model.Workflow

getJsonEscapeFullName.

getJsonEscapeKey() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

getJsonEscapeKey.

getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Experiment

getJsonEscapeName.

getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.IUS

getJsonEscapeName.

getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Lane

getJsonEscapeName.

getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Sample

getJsonEscapeName.

getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.SequencerRun

getJsonEscapeName.

getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Workflow

getJsonEscapeName.

getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

getJsonEscapeName.

getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Experiment

getJsonEscapeTitle.

getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Sample

getJsonEscapeTitle.

getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Study

getJsonEscapeTitle.

getJsonEscapeType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

getJsonEscapeType.

getJsonEscapeValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

getJsonEscapeValue.

getJsonEscapeValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

getJsonEscapeValue.

getKey() - Method in class io.seqware.webservice.generated.model.WorkflowParam

getKey() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

getKey() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Getter for the field key.

getKey() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

Getter for the field key.

getKey() - Method in enum net.sourceforge.seqware.common.util.maptools.ReservedIniKeys

getKey() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument

Getter for the field key.

getKey() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile

Getter for the field key.

getKeyValueFromFile(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

getKeyValueFromFile.

getLabel() - Method in class io.seqware.webservice.generated.model.ExperimentLink

getLabel() - Method in class io.seqware.webservice.generated.model.IusLink

getLabel() - Method in class io.seqware.webservice.generated.model.LaneLink

getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingIus

getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingLanes

getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingSamples

getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingStudies

getLabel() - Method in class io.seqware.webservice.generated.model.SampleLink

getLabel() - Method in class io.seqware.webservice.generated.model.StudyLink

getLabel() - Method in class net.sourceforge.seqware.common.model.ExperimentLink

Getter for the field label.

getLabel() - Method in class net.sourceforge.seqware.common.model.IUSLink

Getter for the field label.

getLabel() - Method in class net.sourceforge.seqware.common.model.LaneLink

Getter for the field label.

getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments

Getter for the field label.

getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingIus

Getter for the field label.

getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes

Getter for the field label.

getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples

Getter for the field label.

getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Getter for the field label.

getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies

Getter for the field label.

getLabel() - Method in class net.sourceforge.seqware.common.model.SampleLink

Getter for the field label.

getLabel() - Method in class net.sourceforge.seqware.common.model.StudyLink

Getter for the field label.

getLane(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getLane.

getLane(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getLane(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getLane(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getLane() - Method in class net.sourceforge.seqware.common.model.FileReportRow

Getter for the field lane.

getLane() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field lane.

getLane() - Method in class net.sourceforge.seqware.common.model.LaneAttribute

Getter for the field lane.

getLane() - Method in class net.sourceforge.seqware.common.model.LaneLink

Getter for the field lane.

getLane() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes

Getter for the field lane.

getLane() - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Getter for the field lane.

getLane() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId

Getter for the field lane.

getLane() - Method in class net.sourceforge.seqware.common.model.ShareLane

Getter for the field lane.

getLane() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

getLane() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem

Getter for the field lane.

getLane1() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field lane1.

getLane2() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field lane2.

getLane3() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field lane3.

getLane4() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field lane4.

getLane5() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field lane5.

getLane6() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field lane6.

getLane7() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field lane7.

getLane8() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field lane8.

getLane_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Getter for the field lane_url.

getLaneAttributeCollection() - Method in class io.seqware.webservice.generated.model.Lane

getLaneAttributeId() - Method in class io.seqware.webservice.generated.model.LaneAttribute

getLaneAttributeId() - Method in class net.sourceforge.seqware.common.model.LaneAttribute

Getter for the field laneAttributeId.

getLaneAttributes() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field laneAttributes.

getLaneAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

getLaneCollection() - Method in class io.seqware.webservice.generated.model.LaneType

getLaneCollection() - Method in class io.seqware.webservice.generated.model.LibrarySelection

getLaneCollection() - Method in class io.seqware.webservice.generated.model.LibrarySource

getLaneCollection() - Method in class io.seqware.webservice.generated.model.LibraryStrategy

getLaneCollection() - Method in class io.seqware.webservice.generated.model.Organism

getLaneCollection() - Method in class io.seqware.webservice.generated.model.Registration

getLaneCollection() - Method in class io.seqware.webservice.generated.model.Sample

getLaneCollection() - Method in class io.seqware.webservice.generated.model.SequencerRun

getLaneCollection() - Method in class io.seqware.webservice.generated.model.StudyType

getLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO

Getter for the field laneCount.

getLaneCycleDescriptor() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Get the value of laneCycleDescriptor

getLaneDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Get the value of laneDescription

getLaneHtml(Lane, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil

getLaneHtml.

getLaneHtml(Lane, Registration, Integer) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil

getLaneHtml.

getLaneId() - Method in class io.seqware.webservice.generated.model.FileReport

getLaneId() - Method in class io.seqware.webservice.generated.model.Ius

getLaneId() - Method in class io.seqware.webservice.generated.model.Lane

getLaneId() - Method in class io.seqware.webservice.generated.model.LaneAttribute

getLaneId() - Method in class io.seqware.webservice.generated.model.LaneLink

getLaneId() - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns

getLaneId() - Method in class io.seqware.webservice.generated.model.ProcessingLanes

getLaneId() - Method in class io.seqware.webservice.generated.model.SampleReport

getLaneId() - Method in class io.seqware.webservice.generated.model.ShareLane

getLaneId() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field laneId.

getLaneIndex() - Method in class io.seqware.webservice.generated.model.Lane

getLaneIndex() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field laneIndex.

getLaneLinkCollection() - Method in class io.seqware.webservice.generated.model.Lane

getLaneLinkId() - Method in class io.seqware.webservice.generated.model.LaneLink

getLaneLinkId() - Method in class net.sourceforge.seqware.common.model.LaneLink

Getter for the field laneLinkId.

getLaneLinks() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field laneLinks.

getLaneName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

getLaneName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Get the value of laneName

getLaneNumber() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Get the value of laneNumber

getLanes() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field lanes.

getLanes() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field lanes.

getLanes() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field lanes.

getLanes() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field lanes.

getLanes() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field lanes.

getLanes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of lanes

getLaneService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.validation.LaneValidator

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Getter for the field laneService.

getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Getter for the field laneService.

getLaneServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getLaneServiceBean.

getLanesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Get Lanes from a sequencer run.

getLanesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getLanesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getLanesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getLaneSkip() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Get the value of laneSkip

getLaneSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

getLaneSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

getLaneTypeId() - Method in class io.seqware.webservice.generated.model.LaneType

getLaneWorkflowRunsCollection() - Method in class io.seqware.webservice.generated.model.Lane

getLaneWorkflowRunsCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getLaneWorkflowRunsId() - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns

getLastName() - Method in class io.seqware.webservice.generated.model.Registration

getLastName() - Method in class net.sourceforge.seqware.common.model.Registration

Getter for the field lastName.

getLastName() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto

Getter for the field lastName.

getLastUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Registration

getLayout() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

getLayout() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Getter for the field layout.

getLength() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

getLength() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Getter for the field length.

getLibraries() - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl

Returns a complete list of libraries.

getLibraries(Map<String, String>) - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl

Returns a list of libraries that match all attributes provided in the give attributes Map.

getLibraries() - Method in interface net.sourceforge.seqware.common.business.LibraryService

Returns a complete list of libraries.

getLibraries(Map<String, String>) - Method in interface net.sourceforge.seqware.common.business.LibraryService

Returns a list of libraries that match all attributes provided in the give attributes Map.

getLibraries(String, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate

Returns list of libraries that contain the attribute attributeName=attributeValue.

getLibraries() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate

Returns a complete list of libraries.

getLibraries(String, String) - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO

Returns list of libraries that contain the attribute attributeName=attributeValue.

getLibraries() - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO

Returns a complete list of libraries.

getLibraries() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrariesResource

getLibraries.

getLibraryId() - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto

Getter for the field libraryId.

getLibrarySamples() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Getter for the field librarySamples.

getLibrarySelection() - Method in class io.seqware.webservice.generated.model.Lane

getLibrarySelection() - Method in class net.sourceforge.seqware.common.model.Lane

getLibrarySelectionAcc() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Get the value of librarySelectionAcc

getLibrarySelectionId() - Method in class io.seqware.webservice.generated.model.LibrarySelection

getLibrarySelectionId() - Method in class net.sourceforge.seqware.common.model.LibrarySelection

Getter for the field librarySelectionId.

getLibrarySelections() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getLibrarySelections.

getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getLibrarySelectionService() - Method in class net.sourceforge.seqware.common.ContextImpl

getLibrarySelectionService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Getter for the field librarySelectionService.

getLibrarySelectionService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController

Getter for the field librarySelectionService.

getLibrarySelectionServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getLibrarySelectionServiceBean.

getLibraryService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field libraryService.

getLibraryServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getLibraryServiceBean.

getLibrarySizeCode() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

getLibrarySource() - Method in class io.seqware.webservice.generated.model.Lane

getLibrarySource() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getLibrarySource.

getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getLibrarySource() - Method in class net.sourceforge.seqware.common.model.Lane

getLibrarySourceAcc() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Get the value of librarySourceAcc

getLibrarySourceId() - Method in class io.seqware.webservice.generated.model.LibrarySource

getLibrarySourceId() - Method in class net.sourceforge.seqware.common.model.LibrarySource

Getter for the field librarySourceId.

getLibrarySourceService() - Method in class net.sourceforge.seqware.common.ContextImpl

getLibrarySourceService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Getter for the field librarySourceService.

getLibrarySourceService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController

Getter for the field librarySourceService.

getLibrarySourceServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getLibrarySourceServiceBean.

getLibrarySourceTemplateType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Get the value of librarySourceTemplateType

getLibraryStrategies() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getLibraryStrategies.

getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getLibraryStrategy() - Method in class io.seqware.webservice.generated.model.Lane

getLibraryStrategy() - Method in class net.sourceforge.seqware.common.model.Lane

getLibraryStrategyAcc() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Get the value of libraryStrategyAcc

getLibraryStrategyId() - Method in class io.seqware.webservice.generated.model.LibraryStrategy

getLibraryStrategyId() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy

Getter for the field libraryStrategyId.

getLibraryStrategyService() - Method in class net.sourceforge.seqware.common.ContextImpl

getLibraryStrategyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Getter for the field libraryStrategyService.

getLibraryStrategyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController

Getter for the field libraryStrategyService.

getLibraryStrategyServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getLibraryStrategyServiceBean.

getLibraryType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

getLibraryType() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Getter for the field libraryType.

getLimsAdmin() - Method in class io.seqware.webservice.generated.model.Registration

getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentLibraryDesignList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignReadSpecList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.FileList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.IntegerList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.IUSList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.LaneList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.LibrarySourceList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.OrganismList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.PlatformList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.SampleList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.StudyList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.StudyTypeList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList

getList.

getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2

getList.

getLocalhost(OptionSet) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

Get the localhost and a return value describing the failure condition if we are unable to get the localhost

getLocalhost() - Static method in class net.sourceforge.seqware.pipeline.plugins.ITUtility

getLock() - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock

Deprecated.

Lock file, do not clear on exit

getLock(boolean) - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock

Deprecated.

Lock file, but give option to free lock when the JVM exits.

getLock(int, int) - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock

Deprecated.

getLock.

getLongName() - Method in class net.sourceforge.seqware.common.model.Platform

getLongName.

getLookupToken() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine

An engine-specific token for this workflow run that can be used to lookup relevant runtime data.

getLookupToken() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine

getLookupToken() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine

getMainClass() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

return the main class for a Java job, or the script.pl for a perl Job

getMapred_job_tracker() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getMaxMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

getMaxMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command

getMaxMemory() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

getMd5sum() - Method in class io.seqware.webservice.generated.model.File

getMd5sum() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field md5sum.

getMd5sum() - Method in class net.sourceforge.seqware.common.module.FileMetadata

getMd5sum() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

getMd5sum() - Method in class net.sourceforge.seqware.webservice.dto.FileDto

Getter for the field md5sum.

getMeaning() - Method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus

getMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getMemReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field memReq.

getMetadata() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

Getter for the field metadata.

getMetadata() - Method in class net.sourceforge.seqware.pipeline.module.Module

Getter for the field metadata.

getMetadata() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker

getMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB

getMetadata.

getMetadata(long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB

getMetadata.

getMetadata_output_dir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getMetadata_output_file_prefix() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getMetadataOutputPrefix() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob

getMetadataOutputPrefix() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob

getMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

getMetaType() - Method in class io.seqware.webservice.generated.model.File

getMetaType() - Method in class io.seqware.webservice.generated.model.FileType

getMetaType() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field metaType.

getMetaType() - Method in class net.sourceforge.seqware.common.model.FileType

Getter for the field metaType.

getMetaType() - Method in class net.sourceforge.seqware.common.module.FileMetadata

getMetaType() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

getMetaType() - Method in class net.sourceforge.seqware.webservice.dto.FileDto

Getter for the field metaType.

getMimeType() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

getModelAndView(String, ModelAndView) - Static method in class net.sourceforge.solexatools.util.StudyBuildTree

getModelAndView.

getModelId() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

getModelId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

getModelId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

getModelId() - Method in class net.sourceforge.seqware.common.model.LibrarySelection

getModelId() - Method in class net.sourceforge.seqware.common.model.LibrarySource

getModelId() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy

getModelId() - Method in class net.sourceforge.seqware.common.model.Organism

getModelId() - Method in class net.sourceforge.seqware.common.model.Platform

getModelId() - Method in interface net.sourceforge.seqware.common.model.SecondTierModel

Get the id for this model

getModelId() - Method in class net.sourceforge.seqware.common.model.StudyType

getModuleType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule

Getter for the field moduleType.

getName() - Method in class io.seqware.webservice.generated.model.Experiment

getName() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

getName() - Method in class io.seqware.webservice.generated.model.Ius

getName() - Method in class io.seqware.webservice.generated.model.Lane

getName() - Method in class io.seqware.webservice.generated.model.LaneType

getName() - Method in class io.seqware.webservice.generated.model.LibrarySelection

getName() - Method in class io.seqware.webservice.generated.model.LibrarySource

getName() - Method in class io.seqware.webservice.generated.model.LibraryStrategy

getName() - Method in class io.seqware.webservice.generated.model.Organism

getName() - Method in class io.seqware.webservice.generated.model.Platform

getName() - Method in class io.seqware.webservice.generated.model.Sample

getName() - Method in class io.seqware.webservice.generated.model.SequencerRun

getName() - Method in class io.seqware.webservice.generated.model.StudyType

getName() - Method in class io.seqware.webservice.generated.model.Workflow

getName() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getName() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.model.LibrarySelection

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.model.LibrarySource

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.model.Organism

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.model.Platform

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.model.StudyType

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Get the value of name

getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule

getName.

getName() - Method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Module

getName.

getName() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Getter for the field name.

getName() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto

Getter for the field name.

getName() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel

getNameNode() - Method in class net.sourceforge.seqware.common.business.UploadFile

Getter for the field nameNode.

getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile

getNamespace.

getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement

getNcbiTaxid() - Method in class io.seqware.webservice.generated.model.Organism

getNcbiTaxId() - Method in class net.sourceforge.seqware.common.model.Organism

Getter for the field ncbiTaxId.

getNcbiTaxonomyId() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto

Getter for the field ncbiTaxonomyId.

getNetwork() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getNetworkReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field networkReq.

getNewType() - Method in class io.seqware.webservice.generated.model.Study

getNewType() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field newType.

getNodeHtml(Processing, Registration, String, boolean, boolean, boolean, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil

getNodeHtml.

getNodeHtml(Processing, Registration) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil

getNodeHtml.

getNodeIds(Object) - Static method in class net.sourceforge.solexatools.util.FindChildUtil

getNodeIds.

getNominalLength() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

getNominalLength() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Getter for the field nominalLength.

getNominalSdev() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

getNominalSdev() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Getter for the field nominalSdev.

getNoOp() - Static method in class net.sourceforge.seqware.common.metadata.MetadataFactory

getNotes() - Method in class io.seqware.webservice.generated.model.Invoice

getNotes() - Method in class net.sourceforge.seqware.common.model.Invoice

Getter for the field notes.

getNotRunned() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Getter for the field notRunned.

getOffspringProcessings() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field offspringProcessings.

getOkTo() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

getOOZIE_APP_PATH() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getOOZIE_APP_ROOT() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getOOZIE_JOBTRACKER() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getOOZIE_NAMENODE() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getOOZIE_QUEUENAME() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getOOZIE_URL() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getOOZIE_WORK_DIR() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getOozieWorkingDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

getOptionParser() - Method in class net.sourceforge.seqware.pipeline.module.Module

getOptionParser.

getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

getOptionParser is an internal method to parse command line args.

getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver

Deprecated.

getOptionParser is an internal method to parse command line args.

getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle

getOptionParser.

getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

getOptionParser.

getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

getOptionParser.

getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

getOptionParser.

getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

getOptionParser.

getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory

getOrganism() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field organism.

getOrganism() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field organism.

getOrganism() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Getter for the field organism.

getOrganismId() - Method in class io.seqware.webservice.generated.model.Lane

getOrganismId() - Method in class io.seqware.webservice.generated.model.Organism

getOrganismId() - Method in class io.seqware.webservice.generated.model.Sample

getOrganismId() - Method in class net.sourceforge.seqware.common.model.Organism

Getter for the field organismId.

getOrganismId() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field organismId.

getOrganismId() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

getOrganisms() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getOrganisms.

getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getOrganismService() - Method in class net.sourceforge.seqware.common.ContextImpl

getOrganismService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController

Getter for the field organismService.

getOrganismService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController

Getter for the field organismService.

getOrganismServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getOrganismServiceBean.

getOriginalFileName() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Getter for the field originalFileName.

getOs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

getOutput() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread

getOutputDir() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

Getter for the field outputDir.

getOutputDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob

getOutputDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob

getOutputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Getter for the field outputFiles.

getOutputLineCapacity() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command

getOutputPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

getOwner() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field owner.

getOwner() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field owner.

getOwner() - Method in class net.sourceforge.seqware.common.model.Invoice

Getter for the field owner.

getOwner() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field owner.

getOwner() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field owner.

getOwner() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field owner.

getOwner() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field owner.

getOwner() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field owner.

getOwner() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field owner.

getOwner() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field owner.

getOwner() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field owner.

getOwner() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field owner.

getOwner() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Getter for the field owner.

getOwnerId() - Method in class io.seqware.webservice.generated.model.Experiment

getOwnerId() - Method in class io.seqware.webservice.generated.model.File

getOwnerId() - Method in class io.seqware.webservice.generated.model.Invoice

getOwnerId() - Method in class io.seqware.webservice.generated.model.Ius

getOwnerId() - Method in class io.seqware.webservice.generated.model.Lane

getOwnerId() - Method in class io.seqware.webservice.generated.model.Processing

getOwnerId() - Method in class io.seqware.webservice.generated.model.Sample

getOwnerId() - Method in class io.seqware.webservice.generated.model.SequencerRun

getOwnerId() - Method in class io.seqware.webservice.generated.model.Study

getOwnerId() - Method in class io.seqware.webservice.generated.model.Workflow

getOwnerId() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getOwnerUserName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

getPage() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid

Getter for the field page.

getPageInfo(HttpServletRequest, String, List, List, String, String, MessageSourceAccessor) - Static method in class net.sourceforge.solexatools.util.PaginationUtil

getPageInfo.

getPageInfoSD(HttpServletRequest, String, List, List, MessageSourceAccessor) - Static method in class net.sourceforge.solexatools.util.PaginationUtil

getPageInfoSD.

getPageNumber(HttpServletRequest, Study, List<Study>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil

getPageNumber.

getPaidAmount() - Method in class io.seqware.webservice.generated.model.Invoice

getPaidAmount() - Method in class net.sourceforge.seqware.common.model.Invoice

Getter for the field paidAmount.

getPairedEnd() - Method in class io.seqware.webservice.generated.model.SequencerRun

getPairedEnd() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field pairedEnd.

getPairedEnd() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field pairedEnd.

getPairedEnd() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

getPairedFilePath() - Method in class io.seqware.webservice.generated.model.SequencerRun

getPairedFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field pairedFilePath.

getPairedFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field pairedFilePath.

getPairedOrientation() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

getPairedOrientation() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Getter for the field pairedOrientation.

getParameters() - Method in class io.seqware.webservice.generated.model.Processing

getParameters() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field parameters.

getParameters() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field parameters.

getParameters() - Method in class net.sourceforge.seqware.pipeline.module.Module

Getter for the field parameters.

getParams() - Method in class net.sourceforge.solexatools.util.SummaryLine

Getter for the field params.

getParentAccessions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getParentAccessions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

getParentAccessions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

getParentId() - Method in class io.seqware.webservice.generated.model.ProcessingRelationship

getParentId() - Method in class io.seqware.webservice.generated.model.SampleRelationship

getParentId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy

getParentLane(Processing, Integer) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil

getParentLane.

getParentProcessing(Processing, Integer) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil

getParentProcessing.

getParentProcessingAccession() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

getParentProcessingAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

Getter for the field parentProcessingAccession.

getParentProcessings() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Getter for the field parentProcessings.

getParents() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field parents.

getParents() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field parents.

getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

add all parent jobs

getParents() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

getParentSample() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Get the value of parentSample

getParentSamplesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Get the parent samples of a sample.

getParentSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getParentSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getParentSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getParentUrls() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Getter for the field parentUrls.

getParentWorkflowAccessions() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

getPassword() - Method in class io.seqware.webservice.generated.model.Registration

getPassword() - Method in class net.sourceforge.seqware.common.model.Registration

Getter for the field password.

getPasswordHint() - Method in class io.seqware.webservice.generated.model.Registration

getPasswordHint() - Method in class net.sourceforge.seqware.common.model.Registration

Getter for the field passwordHint.

getPathToFirstFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field pathToFirstFile.

getPathToSecondFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field pathToSecondFile.

getPayee() - Method in class io.seqware.webservice.generated.model.Registration

getPeakMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getPeakThreads() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getPegasusConfigDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getPending() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Getter for the field pending.

getPermanentBundleLocation() - Method in class io.seqware.webservice.generated.model.Workflow

getPermanentBundleLocation() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field permanentBundleLocation.

getPermBundleLocation() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field permBundleLocation.

getPfn() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

getPipelineJarPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag

getPlatform() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field platform.

getPlatform() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field platform.

getPlatform() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field platform.

getPlatformId() - Method in class io.seqware.webservice.generated.model.Experiment

getPlatformId() - Method in class io.seqware.webservice.generated.model.Platform

getPlatformId() - Method in class io.seqware.webservice.generated.model.SequencerRun

getPlatformId() - Method in class net.sourceforge.seqware.common.model.Platform

Getter for the field platformId.

getPlatformId() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

getPlatformInt() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field platformInt.

getPlatformInt() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field platformInt.

getPlatforms() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getPlatforms.

getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getPlatformService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field platformService.

getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Getter for the field platformService.

getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController

Getter for the field platformService.

getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Getter for the field platformService.

getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController

Getter for the field platformService.

getPlatformServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getPlatformServiceBean.

getPOSTGRE_DB() - Static method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

getPOSTGRE_PASSWORD() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

getPOSTGRE_USER() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

getPricePerUnit() - Method in class io.seqware.webservice.generated.model.Expense

getPricePerUnit() - Method in class net.sourceforge.seqware.common.model.Expense

Getter for the field pricePerUnit.

getPricePerUnitString() - Method in class net.sourceforge.seqware.common.model.Expense

Getter for the field pricePerUnit.

getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.BundleDir_Check

getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.CLICheck

getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_Check

getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_WS_ConsistencyCheck

getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.HDFS_Check

getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.Oozie_Check

getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.Script_Check

getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.TutorialCheck

getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.WS_Check

getPriority() - Method in interface io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface

Indicate the priority of the check, higher is later

getPrivate() - Method in class net.sourceforge.seqware.common.model.Workflow

getPrivate.

getProcess() - Method in class io.seqware.webservice.generated.model.SequencerRun

getProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field process.

getProcessedCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

getProcessedCnt.

getProcessedCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

Deprecated.

getProcessedCnt() - Method in class net.sourceforge.seqware.common.model.Lane

getProcessedCnt.

getProcessedCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun

getProcessedCnt.

getProcessedCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field processedCount.

getProcessExitStatus() - Method in class io.seqware.webservice.generated.model.Processing

getProcessExitStatus() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field processExitStatus.

getProcessExitStatus() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field processExitStatus.

getProcessing(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getProcessing.

getProcessing(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getProcessing(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getProcessing(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getProcessing() - Method in class net.sourceforge.seqware.common.model.FileReportRow

Getter for the field processing.

getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

Getter for the field processing.

getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments

Getter for the field processing.

getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingIus

Getter for the field processing.

getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes

Getter for the field processing.

getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples

Getter for the field processing.

getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Getter for the field processing.

getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies

Getter for the field processing.

getProcessing() - Method in class net.sourceforge.seqware.common.model.ShareProcessing

Getter for the field processing.

getProcessingAccession() - Method in class net.sourceforge.seqware.pipeline.module.Module

Getter for the field processingAccession.

getProcessingAttributeCollection() - Method in class io.seqware.webservice.generated.model.Processing

getProcessingAttributeId() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute

getProcessingAttributeId() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

Getter for the field processingAttributeId.

getProcessingAttributes() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field processingAttributes.

getProcessingByChildId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship

Getter for the field processingByChildId.

getProcessingByParentId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship

Getter for the field processingByParentId.

getProcessingCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

getProcessingCnt.

getProcessingCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

Deprecated.

getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.Lane

getProcessingCnt.

getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun

getProcessingCnt.

getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

getProcessingCnt.

getProcessingCollection() - Method in class io.seqware.webservice.generated.model.Registration

getProcessingCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getProcessingCollection1() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getProcessingCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field processingCount.

getProcessingExperimentsCollection() - Method in class io.seqware.webservice.generated.model.Experiment

getProcessingExperimentsCollection() - Method in class io.seqware.webservice.generated.model.Processing

getProcessingExperimentServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getProcessingExperimentServiceBean.

getProcessingExperimentsId() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

getProcessingExperimentsId() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments

Getter for the field processingExperimentsId.

getProcessingExperimentsService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field processingExperimentsService.

getProcessingFilesCollection() - Method in class io.seqware.webservice.generated.model.File

getProcessingFilesCollection() - Method in class io.seqware.webservice.generated.model.Processing

getProcessingFilesId() - Method in class io.seqware.webservice.generated.model.ProcessingFiles

getProcessingHtml(Processing, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil

getProcessingHtml.

getProcessingId() - Method in class io.seqware.webservice.generated.model.FileReport

getProcessingId() - Method in class io.seqware.webservice.generated.model.Processing

getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute

getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingFiles

getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingIus

getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingLanes

getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingSamples

getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingStudies

getProcessingId() - Method in class io.seqware.webservice.generated.model.ShareProcessing

getProcessingId() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field processingId.

getProcessingIusCollection() - Method in class io.seqware.webservice.generated.model.Ius

getProcessingIusCollection() - Method in class io.seqware.webservice.generated.model.Processing

getProcessingIusId() - Method in class io.seqware.webservice.generated.model.ProcessingIus

getProcessingIusId() - Method in class net.sourceforge.seqware.common.model.ProcessingIus

Getter for the field processingIusId.

getProcessingIusService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field processingIusService.

getProcessingIUSServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getProcessingIUSServiceBean.

getProcessingLanesCollection() - Method in class io.seqware.webservice.generated.model.Lane

getProcessingLanesCollection() - Method in class io.seqware.webservice.generated.model.Processing

getProcessingLaneService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field processingLaneService.

getProcessingLaneServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getProcessingLaneServiceBean.

getProcessingLanesId() - Method in class io.seqware.webservice.generated.model.ProcessingLanes

getProcessingLanesId() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes

Getter for the field processingLanesId.

getProcessingRelations(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getProcessingRelations.

getProcessingRelations(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getProcessingRelations(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getProcessingRelations(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getProcessingRelationshipCollection() - Method in class io.seqware.webservice.generated.model.Processing

getProcessingRelationshipCollection1() - Method in class io.seqware.webservice.generated.model.Processing

getProcessingRelationshipId() - Method in class io.seqware.webservice.generated.model.ProcessingRelationship

getProcessingRelationshipId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship

Getter for the field processingRelationshipId.

getProcessingRelationshipService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field processingRelationshipService.

getProcessingRelationshipServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getProcessingRelationshipServiceBean.

getProcessings() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field processings.

getProcessings() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field processings.

getProcessings() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field processings.

getProcessings() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field processings.

getProcessings() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field processings.

getProcessings() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field processings.

getProcessings() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field processings.

getProcessings() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field processings.

getProcessings() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field processings.

getProcessingSamplesCollection() - Method in class io.seqware.webservice.generated.model.Processing

getProcessingSamplesCollection() - Method in class io.seqware.webservice.generated.model.Sample

getProcessingSampleServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getProcessingSampleServiceBean.

getProcessingSamplesId() - Method in class io.seqware.webservice.generated.model.ProcessingSamples

getProcessingSamplesId() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples

Getter for the field processingSamplesId.

getProcessingSamplesService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field processingSamplesService.

getProcessingsByWorkflow(WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems

getProcessingsByWorkflow.

getProcessingSequencerRunsCollection() - Method in class io.seqware.webservice.generated.model.Processing

getProcessingSequencerRunsCollection() - Method in class io.seqware.webservice.generated.model.SequencerRun

getProcessingSequencerRunService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field processingSequencerRunService.

getProcessingSequencerRunsId() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

getProcessingSequencerRunsId() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Getter for the field processingSequencerRunsId.

getProcessingSequencerRunsServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getProcessingSequencerRunsServiceBean.

getProcessingService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Getter for the field processingService.

getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Getter for the field processingService.

getProcessingServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getProcessingServiceBean.

getProcessingStudiesCollection() - Method in class io.seqware.webservice.generated.model.Processing

getProcessingStudiesCollection() - Method in class io.seqware.webservice.generated.model.Study

getProcessingStudiesId() - Method in class io.seqware.webservice.generated.model.ProcessingStudies

getProcessingStudiesId() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies

Getter for the field processingStudiesId.

getProcessingStudiesService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field processingStudiesService.

getProcessingStudiesServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getProcessingStudiesServiceBean.

getProcStatuses(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

getProcStatuses.

getProcStatuses(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

Deprecated.

getProjectCode() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

getProjectId() - Method in class io.seqware.webservice.generated.model.Study

getProjectId() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field projectId.

getProperty(String) - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools

getProperty.

getProperty(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

get the user defined INI files properties

getProperty(String) - Static method in class net.sourceforge.seqware.queryengine.webservice.util.EnvUtil

getProperty.

getProvisionedPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

getPublic() - Method in class net.sourceforge.seqware.common.model.Workflow

getPublic.

getQsubOptions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

getQualityMultiplier() - Method in class io.seqware.webservice.generated.model.Experiment

getQualityMultiplier() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field qualityMultiplier.

getQualityNumberOfLevels() - Method in class io.seqware.webservice.generated.model.Experiment

getQualityNumberOfLevels() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field qualityNumberOfLevels.

getQualityScorer() - Method in class io.seqware.webservice.generated.model.Experiment

getQualityScorer() - Method in class io.seqware.webservice.generated.model.SequencerRun

getQualityScorer() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field qualityScorer.

getQualityType() - Method in class io.seqware.webservice.generated.model.Experiment

getQualityType() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field qualityType.

getQueryValue(String) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet

getQueue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

getQueue() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

getRandom() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getReadClass() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

getReadClass() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Getter for the field readClass.

getReader() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread

Getter for the field reader.

getReadIndex() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

getReadIndex() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Getter for the field readIndex.

getReadLabel() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

getReadLabel() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Getter for the field readLabel.

getReadSpec() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

getReadSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Getter for the field readSpec.

getReadSpecs() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Getter for the field readSpecs.

getReadsPerSpot() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

getReadsPerSpot() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Getter for the field readsPerSpot.

getReadType() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

getReadType() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Getter for the field readType.

getReadyToProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field readyToProcess.

getRefLane() - Method in class io.seqware.webservice.generated.model.SequencerRun

getRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field refLane.

getRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field refLane.

getRegions() - Method in class io.seqware.webservice.generated.model.Lane

getRegions() - Method in class io.seqware.webservice.generated.model.Sample

getRegions() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field regions.

getRegions() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field regions.

getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareExperiment

Getter for the field registration.

getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareFile

Getter for the field registration.

getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareLane

Getter for the field registration.

getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareProcessing

Getter for the field registration.

getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareSample

Getter for the field registration.

getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareStudy

Getter for the field registration.

getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

Getter for the field registration.

getRegistration(HttpServletRequest) - Static method in class net.sourceforge.solexatools.Security

getRegistration.

getRegistrationId() - Method in class io.seqware.webservice.generated.model.Registration

getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareExperiment

getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareFile

getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareLane

getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareProcessing

getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareSample

getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareStudy

getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

getRegistrationId() - Method in class net.sourceforge.seqware.common.model.Registration

Getter for the field registrationId.

getRegistrationService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field registrationService.

getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController

Getter for the field registrationService.

getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController

Getter for the field registrationService.

getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.LoginController

Getter for the field registrationService.

getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController

Getter for the field registrationService.

getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController

Getter for the field registrationService.

getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController

Getter for the field registrationService.

getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController

Getter for the field registrationService.

getRegistrationServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getRegistrationServiceBean.

getRelationship() - Method in class io.seqware.webservice.generated.model.ProcessingRelationship

getRelationship() - Method in class io.seqware.webservice.generated.model.SampleRelationship

getRelationship() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship

Getter for the field relationship.

getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.FileReportService

getReportForSequencerRun.

getReportForSequencerRun(SequencerRun, String, String) - Method in interface net.sourceforge.seqware.common.business.FileReportService

getReportForSequencerRun.

getReportForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.FileReportService

getReportForSequencerRun.

getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl

getReportForSequencerRun.

getReportForSequencerRun(SequencerRun, String, String) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl

getReportForSequencerRun.

getReportForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl

getReportForSequencerRun.

getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO

getReportForSequencerRun.

getReportForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO

getReportForSequencerRun.

getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate

getReportForSequencerRun.

getReportForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate

getReportForSequencerRun.

getReportForSequencerRuns(String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO

getReportForSequencerRuns.

getReportForSequencerRuns(String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate

getReportForSequencerRuns.

getReportForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.FileReportService

getReportForStudy.

getReportForStudy(Study, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.FileReportService

getReportForStudy.

getReportForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl

getReportForStudy.

getReportForStudy(Study, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl

getReportForStudy.

getReportForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO

getReportForStudy.

getReportForStudy(Study, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO

getReportForStudy.

getReportForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate

getReportForStudy.

getReportForStudy(Study, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate

getReportForStudy.

getRepresentation(Document) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools

getRepresentation.

getRequestedTypeList(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.ControllerUtil

getRequestedTypeList.

getRequestedTypeList(HttpServletRequest) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

getRequestedTypeList.

getRequirements() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

get job requirements

getResourceInfo(ApplicationInfo) - Method in class net.sourceforge.seqware.webservice.resources.queries.GenericDBResource

getReturnValue() - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException

Getter for the field returnValue.

getReturnValue() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field returnValue.

getReturnValues() - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Getter for the field returnValues.

getRootProcessing(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

getRootProcessing.

getRootProcessing(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

getRootProcessing.

getRootProcessing(WorkflowRun) - Static method in class net.sourceforge.solexatools.util.FindChildUtil

getRootProcessing.

getRootProcessingName() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

getRootProcessingSwa() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

getRootSample(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

getRootSample.

getRootSample(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService

getRootSample.

getRootSample(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

getRootSample.

getRootSample(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

getRootSample.

getRootSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Getter for the field rootSample.

getRootSamples(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

getRootSamples.

getRootSamples(Study) - Method in interface net.sourceforge.seqware.common.business.SampleService

getRootSamples.

getRootSamples(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

getRootSamples.

getRootSamples(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

getRootSamples.

getRowId() - Method in class io.seqware.webservice.generated.model.FileReport

getRowId() - Method in class io.seqware.webservice.generated.model.SampleReport

getRowId() - Method in class net.sourceforge.seqware.common.model.FileReportRow

Getter for the field rowId.

getRowId() - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Getter for the field rowId.

getRows() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid

Getter for the field rows.

getRowsForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

getRowsForSequencerRun.

getRowsForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

getRowsForSequencerRun.

getRowsForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

getRowsForSequencerRun.

getRowsForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

getRowsForSequencerRun.

getRowsWithSequencerRuns() - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

getRowsWithSequencerRuns.

getRowsWithSequencerRuns() - Method in interface net.sourceforge.seqware.common.business.SampleReportService

getRowsWithSequencerRuns.

getRowsWithSequencerRuns() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

getRowsWithSequencerRuns.

getRowsWithSequencerRuns() - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

getRowsWithSequencerRuns.

getRunAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of runAttributes

getRunCenter() - Method in class io.seqware.webservice.generated.model.SequencerRun

getRunCenter() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field runCenter.

getRunCenter() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field runCenter.

getRunDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of runDescription

getRunFilePath() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of runFilePath

getRunInfo() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.CreateFromScratch

getRunName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

getRunName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of runName

getRunningCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

getRunningCount.

getRunningCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService

getRunningCount.

getRunsFromWorkflow(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport

Using a workflow SWID, find all of the workflow runs, and report on each of the workflow runs the files, samples and processing events associated with each.

getRunSkip() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of runSkip

getRunStartTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field runStartTimestamp.

getRunStartTstmp() - Method in class io.seqware.webservice.generated.model.Processing

getRunStartTstmp() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field runStartTstmp.

getRunStopTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field runStopTimestamp.

getRunStopTstmp() - Method in class io.seqware.webservice.generated.model.Processing

getRunStopTstmp() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field runStopTstmp.

getRunSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

getS3InputStream(String, int, long, String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

getS3InputStream.

getS3InputStream(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

getS3InputStream.

getS3Url(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

getS3Url.

getS3Url(String, String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

getS3Url.

getSample() - Method in class net.sourceforge.seqware.common.model.FileReportRow

Getter for the field sample.

getSample() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field sample.

getSample() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field sample.

getSample() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples

Getter for the field sample.

getSample() - Method in class net.sourceforge.seqware.common.model.SampleAttribute

Getter for the field sample.

getSample() - Method in class net.sourceforge.seqware.common.model.SampleLink

Getter for the field sample.

getSample() - Method in class net.sourceforge.seqware.common.model.SampleSearch

Getter for the field sample.

getSample() - Method in class net.sourceforge.seqware.common.model.ShareSample

Getter for the field sample.

getSample() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field sample.

getSample() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Getter for the field sample.

getSample() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

getSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Getter for the field sample.

getSample_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Getter for the field sample_url.

getSampleAttributeCollection() - Method in class io.seqware.webservice.generated.model.Sample

getSampleAttributeId() - Method in class io.seqware.webservice.generated.model.SampleAttribute

getSampleAttributeId() - Method in class net.sourceforge.seqware.common.model.SampleAttribute

Getter for the field sampleAttributeId.

getSampleAttributes() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field sampleAttributes.

getSampleAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Get the value of sampleAttributes

getSampleByName(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getSampleByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getSampleByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getSampleByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getSampleCode() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field sampleCode.

getSampleCollection() - Method in class io.seqware.webservice.generated.model.Experiment

getSampleCollection() - Method in class io.seqware.webservice.generated.model.Organism

getSampleCollection() - Method in class io.seqware.webservice.generated.model.Registration

getSampleCollection() - Method in class io.seqware.webservice.generated.model.Sample

getSampleCollection1() - Method in class io.seqware.webservice.generated.model.Sample

getSampleDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Get the value of sampleDescription

getSampleHierarchies() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchies

getSampleHtml(Sample, Registration, String, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil

getSampleHtml.

getSampleHtml(Sample, Registration, Integer) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil

getSampleHtml.

getSampleId() - Method in class io.seqware.webservice.generated.model.FileReport

getSampleId() - Method in class io.seqware.webservice.generated.model.Ius

getSampleId() - Method in class io.seqware.webservice.generated.model.Lane

getSampleId() - Method in class io.seqware.webservice.generated.model.ProcessingSamples

getSampleId() - Method in class io.seqware.webservice.generated.model.Sample

getSampleId() - Method in class io.seqware.webservice.generated.model.SampleAttribute

getSampleId() - Method in class io.seqware.webservice.generated.model.SampleLink

getSampleId() - Method in class io.seqware.webservice.generated.model.SampleSearch

getSampleId() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute

getSampleId() - Method in class io.seqware.webservice.generated.model.ShareSample

getSampleId() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field sampleId.

getSampleId() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field sampleId.

getSampleId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy

getSampleId() - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto

Getter for the field sampleId.

getSampleLinkCollection() - Method in class io.seqware.webservice.generated.model.Sample

getSampleLinkId() - Method in class io.seqware.webservice.generated.model.SampleLink

getSampleLinkId() - Method in class net.sourceforge.seqware.common.model.SampleLink

Getter for the field sampleLinkId.

getSampleLinks() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field sampleLinks.

getSampleName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

getSampleRelationshipCollection() - Method in class io.seqware.webservice.generated.model.Sample

getSampleRelationshipCollection1() - Method in class io.seqware.webservice.generated.model.Sample

getSampleRelationshipId() - Method in class io.seqware.webservice.generated.model.SampleRelationship

getSampleReportService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field sampleReportService.

getSampleReportServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getSampleReportServiceBean.

getSamples() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field samples.

getSamples() - Method in class net.sourceforge.seqware.common.model.Lane

getSamples.

getSamples() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field samples.

getSamples() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field samples.

getSamples() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Get the value of samples

getSampleSearch() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute

Getter for the field sampleSearch.

getSampleSearchAttributeCollection() - Method in class io.seqware.webservice.generated.model.SampleSearch

getSampleSearchAttributeId() - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute

getSampleSearchAttributeId() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute

Getter for the field sampleSearchAttributeId.

getSampleSearchAttributes() - Method in class net.sourceforge.seqware.common.model.SampleSearch

Getter for the field sampleSearchAttributes.

getSampleSearchCollection() - Method in class io.seqware.webservice.generated.model.Sample

getSampleSearchId() - Method in class io.seqware.webservice.generated.model.SampleSearch

getSampleSearchId() - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute

getSampleSearchId() - Method in class net.sourceforge.seqware.common.model.SampleSearch

Getter for the field sampleSearchId.

getSampleSearchService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field sampleSearchService.

getSampleSearchServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getSampleSearchServiceBean.

getSampleService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.validation.SampleValidator

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Getter for the field sampleService.

getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController

Getter for the field sampleService.

getSampleServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getSampleServiceBean.

getSamplesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Get the samples from an experiment.

getSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getSampleSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

getSampleSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

getSampleType() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field sampleType.

getSampleUrl() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto

Getter for the field sampleUrl.

getScientificName() - Method in class io.seqware.webservice.generated.model.Sample

getSelectedIds(HttpServletRequest, String, String[], String[]) - Static method in class net.sourceforge.solexatools.util.BulkUtil

getSelectedIds.

getSelectedWorkflowParamValue(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

getSelectedWorkflowParamValue.

getSelection() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

getSelection() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Getter for the field selection.

getSender() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController

Getter for the field sender.

getSequencer_run_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Getter for the field sequencer_run_url.

getSequencerRun(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getSequencerRun.

getSequencerRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getSequencerRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getSequencerRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getSequencerRun() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field sequencerRun.

getSequencerRun() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Getter for the field sequencerRun.

getSequencerRun() - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Getter for the field sequencerRun.

getSequencerRun() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId

Getter for the field sequencerRun.

getSequencerRun() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

getSequencerRun(Lane) - Static method in class net.sourceforge.solexatools.util.FindRootUtil

getSequencerRun.

getSequencerRun(Processing) - Static method in class net.sourceforge.solexatools.util.FindRootUtil

getSequencerRun.

getSequencerRun() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem

Getter for the field sequencerRun.

getSequencerRunAttributeCollection() - Method in class io.seqware.webservice.generated.model.SequencerRun

getSequencerRunAttributeId() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute

getSequencerRunAttributeId() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

Getter for the field sequencerRunAttributeId.

getSequencerRunAttributes() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field sequencerRunAttributes.

getSequencerRunByName(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getSequencerRunByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getSequencerRunByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getSequencerRunByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getSequencerRunCollection() - Method in class io.seqware.webservice.generated.model.Platform

getSequencerRunCollection() - Method in class io.seqware.webservice.generated.model.Registration

getSequencerRunHtml(SequencerRun, Registration, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil

getSequencerRunHtml.

getSequencerRunId() - Method in class io.seqware.webservice.generated.model.Lane

getSequencerRunId() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

getSequencerRunId() - Method in class io.seqware.webservice.generated.model.SampleReport

getSequencerRunId() - Method in class io.seqware.webservice.generated.model.SequencerRun

getSequencerRunId() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field sequencerRunId.

getSequencerRunId() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field sequencerRunId.

getSequencerRunReport() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getSequencerRunReport.

getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getSequencerRunReport.

getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getSequencerRunReport.

getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getSequencerRunReport.

getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

getSequencerRunReportIds.

getSequencerRunReportIds(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

getSequencerRunReportIds.

getSequencerRunReportIds(SequencerRun, String, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

getSequencerRunReportIds.

getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

getSequencerRunReportIds.

getSequencerRunReportIds(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

getSequencerRunReportIds.

getSequencerRunReportIds(SequencerRun, String, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

getSequencerRunReportIds.

getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

getSequencerRunReportIds.

getSequencerRunReportIds(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

getSequencerRunReportIds.

getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

getSequencerRunReportIds.

getSequencerRunReportIds(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

getSequencerRunReportIds.

getSequencerRuns() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field sequencerRuns.

getSequencerRunService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field sequencerRunService.

getSequencerRunService() - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator

Getter for the field sequencerRunService.

getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController

Getter for the field sequencerRunService.

getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController

Getter for the field sequencerRunService.

getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController

Getter for the field sequencerRunService.

getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO

Getter for the field sequencerRunService.

getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController

Getter for the field sequencerRunService.

getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController

Getter for the field sequencerRunService.

getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController

Getter for the field sequencerRunService.

getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO

Getter for the field sequencerRunService.

getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Getter for the field sequencerRunService.

getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController

Getter for the field sequencerRunService.

getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Getter for the field sequencerRunService.

getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Getter for the field sequencerRunService.

getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController

Getter for the field sequencerRunService.

getSequencerRunServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getSequencerRunServiceBean.

getSequencerRunSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

getSequencerRunValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Getter for the field sequencerRunValidator.

getSequencerRunWizardDTO() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

getSequencerRunWizardDTO.

getSequencerRunWizardValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Getter for the field sequencerRunWizardValidator.

getSequenceSpace() - Method in class io.seqware.webservice.generated.model.Experiment

getSequenceSpace() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field sequenceSpace.

getSEQWARE_DB() - Method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator

getSEQWARE_DB() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

getSEQWARE_DB() - Method in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator

getSEQWARE_PASSWORD() - Method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator

getSEQWARE_PASSWORD() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

getSEQWARE_PASSWORD() - Method in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator

getSEQWARE_USER() - Method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator

getSEQWARE_USER() - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

getSEQWARE_USER() - Method in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator

getSeqware_version() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getSeqwareAccession() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

getSeqwareRevision() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getSeqwareRevision() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field seqwareRevision.

getSeqwareVersion() - Method in class io.seqware.webservice.generated.model.Workflow

getSeqwareVersion() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field seqwareVersion.

getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field serialVersionUID.

getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Getter for the field serialVersionUID.

getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Getter for the field serialVersionUID.

getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Lane

Getter for the field serialVersionUID.

getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Platform

Getter for the field serialVersionUID.

getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Processing

Getter for the field serialVersionUID.

getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Sample

Getter for the field serialVersionUID.

getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field serialVersionUID.

getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field serialVersionUID.

getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Study

Getter for the field serialVersionUID.

getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.StudyType

Getter for the field serialVersionUID.

getSessionFactory() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field sessionFactory.

getSessionFactoryBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getSessionFactoryBean.

getSettings() - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools

The output keys are always uppercase!

getSettingsFilePath() - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools

getSharedStudies() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field sharedStudies.

getSharedWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field sharedWorkflowRuns.

getShareExperimentCollection() - Method in class io.seqware.webservice.generated.model.Experiment

getShareExperimentCollection() - Method in class io.seqware.webservice.generated.model.Registration

getShareExperimentId() - Method in class io.seqware.webservice.generated.model.ShareExperiment

getShareExperimentId() - Method in class net.sourceforge.seqware.common.model.ShareExperiment

Getter for the field shareExperimentId.

getShareFileCollection() - Method in class io.seqware.webservice.generated.model.File

getShareFileCollection() - Method in class io.seqware.webservice.generated.model.Registration

getShareFileId() - Method in class io.seqware.webservice.generated.model.ShareFile

getShareFileId() - Method in class net.sourceforge.seqware.common.model.ShareFile

Getter for the field shareFileId.

getShareLaneCollection() - Method in class io.seqware.webservice.generated.model.Lane

getShareLaneCollection() - Method in class io.seqware.webservice.generated.model.Registration

getShareLaneId() - Method in class io.seqware.webservice.generated.model.ShareLane

getShareLaneId() - Method in class net.sourceforge.seqware.common.model.ShareLane

Getter for the field shareLaneId.

getShareProcessingCollection() - Method in class io.seqware.webservice.generated.model.Processing

getShareProcessingCollection() - Method in class io.seqware.webservice.generated.model.Registration

getShareProcessingId() - Method in class io.seqware.webservice.generated.model.ShareProcessing

getShareProcessingId() - Method in class net.sourceforge.seqware.common.model.ShareProcessing

Getter for the field shareProcessingId.

getShareSampleCollection() - Method in class io.seqware.webservice.generated.model.Registration

getShareSampleCollection() - Method in class io.seqware.webservice.generated.model.Sample

getShareSampleId() - Method in class io.seqware.webservice.generated.model.ShareSample

getShareSampleId() - Method in class net.sourceforge.seqware.common.model.ShareSample

Getter for the field shareSampleId.

getShareStudyCollection() - Method in class io.seqware.webservice.generated.model.Registration

getShareStudyCollection() - Method in class io.seqware.webservice.generated.model.Study

getShareStudyId() - Method in class io.seqware.webservice.generated.model.ShareStudy

getShareStudyId() - Method in class net.sourceforge.seqware.common.model.ShareStudy

Getter for the field shareStudyId.

getShareStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController

Getter for the field shareStudyService.

getShareStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

Getter for the field shareStudyService.

getShareWorkflowRun(String, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate

getShareWorkflowRun.

getShareWorkflowRun(String, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO

getShareWorkflowRun.

getShareWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.Registration

getShareWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getShareWorkflowRunId() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

getShareWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

Getter for the field shareWorkflowRunId.

getShareWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController

Getter for the field shareWorkflowRunService.

getShareWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController

Getter for the field shareWorkflowRunService.

getSingleWorkflowRun(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport

Using a workflow run SWID, report on the files, samples and processing events associated with the run.

getSite() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn

Getter for the field site.

getSize() - Method in class io.seqware.webservice.generated.model.File

getSize() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field size.

getSize() - Method in class net.sourceforge.seqware.common.module.FileMetadata

getSize() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

getSize() - Method in class net.sourceforge.seqware.webservice.dto.FileDto

Getter for the field size.

getSkip() - Method in class io.seqware.webservice.generated.model.File

getSkip() - Method in class io.seqware.webservice.generated.model.Ius

getSkip() - Method in class io.seqware.webservice.generated.model.Lane

getSkip() - Method in class io.seqware.webservice.generated.model.Sample

getSkip() - Method in class io.seqware.webservice.generated.model.SequencerRun

getSkip() - Method in class net.sourceforge.seqware.common.model.File

getSkip() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field skip.

getSkip() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field skip.

getSkip() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field skip.

getSkip() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field skip.

getSkip() - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Getter for the field skip.

getSlide1FilePath() - Method in class io.seqware.webservice.generated.model.SequencerRun

getSlide1LaneCount() - Method in class io.seqware.webservice.generated.model.SequencerRun

getSlide2FilePath() - Method in class io.seqware.webservice.generated.model.SequencerRun

getSlide2LaneCount() - Method in class io.seqware.webservice.generated.model.SequencerRun

getSlideCount() - Method in class io.seqware.webservice.generated.model.SequencerRun

getSlideOneFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field slideOneFilePath.

getSlideOneFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field slideOneFilePath.

getSlideOneLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field slideOneLaneCount.

getSlideOneLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field slideOneLaneCount.

getSlideTwoFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field slideTwoFilePath.

getSlideTwoFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field slideTwoFilePath.

getSlideTwoLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field slideTwoLaneCount.

getSlideTwoLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field slideTwoLaneCount.

getSortKeySample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Getter for the field sortKeySample.

getSource() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

getSource() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Getter for the field source.

getSourcePath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

getSourceReader(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

This attempts to resume if passed in startPosition > 0.

getSpotDesignReadSpec() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field spotDesignReadSpec.

getSql() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

Getter for the field sql.

getStartDate() - Method in class io.seqware.webservice.generated.model.Invoice

getStartDate() - Method in class net.sourceforge.seqware.common.model.Invoice

Getter for the field startDate.

getStartPage() - Method in class net.sourceforge.solexatools.util.PageInfo

Getter for the field startPage.

getState() - Method in class io.seqware.webservice.generated.model.Invoice

getState() - Method in class net.sourceforge.seqware.common.model.Invoice

Getter for the field state.

getStatus() - Method in class io.seqware.webservice.generated.model.Experiment

getStatus() - Method in class io.seqware.webservice.generated.model.Processing

getStatus() - Method in class io.seqware.webservice.generated.model.SampleReport

getStatus() - Method in class io.seqware.webservice.generated.model.SequencerRun

getStatus() - Method in class io.seqware.webservice.generated.model.Study

getStatus() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getStatus(Study, Sample, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

getStatus.

getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

getStatus.

getStatus(Study, Sample, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

getStatus.

getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

getStatus.

getStatus(Study, Sample, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

getStatus.

getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

getStatus.

getStatus(Study, Sample, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

getStatus.

getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

getStatus.

getStatus() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field status.

getStatus() - Method in class net.sourceforge.seqware.common.model.Processing

getStatus() - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Getter for the field status.

getStatus() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field status.

getStatus() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field status.

getStatus() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field status.

getStatus() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field status.

getStatus() - Method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus

getStatus() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of the sequencer run status

getStatusCmd() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getStatusCmd() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field statusCmd.

getStatusCount(Study, WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

Count the number of workflow runs with the given status, under the given study

getStatusCount(Study, WorkflowRunStatus) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

Count the number of workflow runs with the given status, under the given study

getStatusCounts() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools

Getter for the field statusCounts.

getStatuses() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Getter for the field statuses.

getStatusesForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

getStatusesForSequencerRun.

getStatusesForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

getStatusesForSequencerRun.

getStatusesForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

getStatusesForSequencerRun.

getStatusesForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

getStatusesForSequencerRun.

getStatusesForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

getStatusesForStudy.

getStatusesForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

getStatusesForStudy.

getStatusesForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

getStatusesForStudy.

getStatusesForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

getStatusesForStudy.

getStatusesForWorkflow(Study, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

getStatusesForWorkflow.

getStatusesForWorkflow(SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

getStatusesForWorkflow.

getStatusesForWorkflow(Study, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

getStatusesForWorkflow.

getStatusesForWorkflow(SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

getStatusesForWorkflow.

getStatusesForWorkflow(Study, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

getStatusesForWorkflow.

getStatusesForWorkflow(SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

getStatusesForWorkflow.

getStatusesForWorkflow(Study, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

getStatusesForWorkflow.

getStatusesForWorkflow(SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

getStatusesForWorkflow.

getStderr() - Method in class io.seqware.webservice.generated.model.Processing

getStderr() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getStderr() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field stderr.

getStdErr() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field stdErr.

getStderr() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field stderr.

getStderrFile() - Method in class net.sourceforge.seqware.pipeline.module.Module

Getter for the file where the stderr will be redirected.

getStdout() - Method in class io.seqware.webservice.generated.model.Processing

getStdout() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getStdout() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field stdout.

getStdOut() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field stdOut.

getStdout() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field stdout.

getStdoutFile() - Method in class net.sourceforge.seqware.pipeline.module.Module

Getter for the file where the stdout will be redirected.

getStrategy() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

getStrategy() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Getter for the field strategy.

getStrExpectedNumberReads() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field strExpectedNumberReads.

getStrExpectedNumberRuns() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field strExpectedNumberRuns.

getStrExpectedNumReads() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field strExpectedNumReads.

getStrExpectedNumRuns() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field strExpectedNumRuns.

getStrLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO

Getter for the field strLaneCount.

getStrRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field strRefLane.

getStrStartURL() - Method in class net.sourceforge.seqware.common.business.UploadFile

Getter for the field strStartURL.

getStrStartURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field strStartURL.

getStudies() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field studies.

getStudy() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field study.

getStudy() - Method in class net.sourceforge.seqware.common.model.FileReportRow

Getter for the field study.

getStudy() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies

Getter for the field study.

getStudy() - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Getter for the field study.

getStudy() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId

Getter for the field study.

getStudy() - Method in class net.sourceforge.seqware.common.model.StudyAttribute

Getter for the field study.

getStudy() - Method in class net.sourceforge.seqware.common.model.StudyLink

Getter for the field study.

getStudy(Experiment) - Static method in class net.sourceforge.solexatools.util.FindRootUtil

getStudy.

getStudy(Sample) - Static method in class net.sourceforge.solexatools.util.FindRootUtil

getStudy.

getStudy(Lane) - Static method in class net.sourceforge.solexatools.util.FindRootUtil

getStudy.

getStudy(Processing) - Static method in class net.sourceforge.solexatools.util.FindRootUtil

getStudy.

getStudyAttributeCollection() - Method in class io.seqware.webservice.generated.model.Study

getStudyAttributeId() - Method in class io.seqware.webservice.generated.model.StudyAttribute

getStudyAttributeId() - Method in class net.sourceforge.seqware.common.model.StudyAttribute

Getter for the field studyAttributeId.

getStudyAttributes() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field studyAttributes.

getStudyAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of studyAttributes

getStudyByName(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getStudyByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getStudyByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getStudyByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getStudyCenterName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of studyCenterName

getStudyCenterProject() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of studyCenterProject

getStudyCollection() - Method in class io.seqware.webservice.generated.model.Registration

getStudyCollection() - Method in class io.seqware.webservice.generated.model.StudyType

getStudyDAO() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

Getter for the field studyDAO.

getStudyDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of studyDescription

getStudyId() - Method in class io.seqware.webservice.generated.model.Experiment

getStudyId() - Method in class io.seqware.webservice.generated.model.FileReport

getStudyId() - Method in class io.seqware.webservice.generated.model.ProcessingStudies

getStudyId() - Method in class io.seqware.webservice.generated.model.SampleReport

getStudyId() - Method in class io.seqware.webservice.generated.model.ShareStudy

getStudyId() - Method in class io.seqware.webservice.generated.model.Study

getStudyId() - Method in class io.seqware.webservice.generated.model.StudyAttribute

getStudyId() - Method in class io.seqware.webservice.generated.model.StudyLink

getStudyId() - Method in class net.sourceforge.seqware.common.model.ShareStudy

Getter for the field studyId.

getStudyId() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field studyId.

getStudyLinkCollection() - Method in class io.seqware.webservice.generated.model.Study

getStudyLinkId() - Method in class io.seqware.webservice.generated.model.StudyLink

getStudyLinkId() - Method in class net.sourceforge.seqware.common.model.StudyLink

Getter for the field studyLinkId.

getStudyLinks() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field studyLinks.

getStudyService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.validation.StudyValidator

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyTableController

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyTableControllerDetails

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Getter for the field studyService.

getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Getter for the field studyService.

getStudyServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getStudyServiceBean.

getStudySwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

getStudyTitle() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of studyTitle

getStudyType() - Method in class io.seqware.webservice.generated.model.Lane

getStudyType() - Method in class net.sourceforge.seqware.common.model.Lane

getStudyType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

getStudyTypeAcc() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Get the value of studyTypeAcc

getStudyTypeDAO() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

Getter for the field studyTypeDAO.

getStudyTypeId() - Method in class io.seqware.webservice.generated.model.StudyType

getStudyTypeId() - Method in class net.sourceforge.seqware.common.model.StudyType

Getter for the field studyTypeId.

getStudyTypes() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getStudyTypes.

getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getStudyTypeService() - Method in class net.sourceforge.seqware.common.ContextImpl

getStudyTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

Getter for the field studyTypeService.

getStudyTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController

Getter for the field studyTypeService.

getStudyTypeServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getStudyTypeServiceBean.

getStydyHtml(Study, Registration, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil

getStydyHtml.

getStydyHtml(Study, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil

getStydyHtml.

getSubject(String, String, String) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos

getSubject.

getSubjectEmail() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams

Getter for the field subjectEmail.

getSummaryData(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

getSummaryData.

getSummaryLines() - Method in class net.sourceforge.solexatools.util.SummaryData

Getter for the field summaryLines.

getSwa() - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Getter for the field swa.

getSwAccession() - Method in class io.seqware.webservice.generated.model.Expense

getSwAccession() - Method in class io.seqware.webservice.generated.model.Experiment

getSwAccession() - Method in class io.seqware.webservice.generated.model.File

getSwAccession() - Method in class io.seqware.webservice.generated.model.Invoice

getSwAccession() - Method in class io.seqware.webservice.generated.model.Ius

getSwAccession() - Method in class io.seqware.webservice.generated.model.Lane

getSwAccession() - Method in class io.seqware.webservice.generated.model.Processing

getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingIus

getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingLanes

getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingSamples

getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingStudies

getSwAccession() - Method in class io.seqware.webservice.generated.model.Sample

getSwAccession() - Method in class io.seqware.webservice.generated.model.SequencerRun

getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareExperiment

getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareFile

getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareLane

getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareProcessing

getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareSample

getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareStudy

getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

getSwAccession() - Method in class io.seqware.webservice.generated.model.Study

getSwAccession() - Method in class io.seqware.webservice.generated.model.Workflow

getSwAccession() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getSwAccession() - Method in class net.sourceforge.seqware.common.model.Expense

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.Invoice

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingIus

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareExperiment

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareFile

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareLane

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareProcessing

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareSample

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareStudy

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field swAccession.

getSwAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field swAccession.

getSwCluster() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

getSyntax() - Static method in class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator

getSyntax.

getSyntax(OptionParser, String) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner

getSyntax.

getTag() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute

getTag() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute

getTag() - Method in class io.seqware.webservice.generated.model.FileAttribute

getTag() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute

getTag() - Method in class io.seqware.webservice.generated.model.Ius

getTag() - Method in class io.seqware.webservice.generated.model.IusAttribute

getTag() - Method in class io.seqware.webservice.generated.model.LaneAttribute

getTag() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute

getTag() - Method in class io.seqware.webservice.generated.model.SampleAttribute

getTag() - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute

getTag() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute

getTag() - Method in class io.seqware.webservice.generated.model.StudyAttribute

getTag() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute

getTag() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute

getTag() - Method in interface net.sourceforge.seqware.common.model.Attribute

getTag.

getTag() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

Getter for the field tag.

getTag() - Method in class net.sourceforge.seqware.common.model.FileAttribute

getTag.

getTag() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field tag.

getTag() - Method in class net.sourceforge.seqware.common.model.IUSAttribute

getTag.

getTag() - Method in class net.sourceforge.seqware.common.model.LaneAttribute

Getter for the field tag.

getTag() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

getTag.

getTag() - Method in class net.sourceforge.seqware.common.model.SampleAttribute

getTag.

getTag() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute

getTag.

getTag() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

Getter for the field tag.

getTag() - Method in class net.sourceforge.seqware.common.model.StudyAttribute

getTag.

getTag() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute

getTag.

getTag() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute

getTag.

getTag() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit

getTagMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB

getTagMetadata.

getTagMetadata(long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB

getTagMetadata.

getTags() - Method in class io.seqware.webservice.generated.model.Lane

getTags() - Method in class io.seqware.webservice.generated.model.Sample

getTags() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field tags.

getTags() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field tags.

getTags() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

the key-value from metadata.xml

getTagSpec() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

getTagSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Getter for the field tagSpec.

getTargetedResequencing() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Get the value of targetedResequencing

getTaskGroup() - Method in class io.seqware.webservice.generated.model.Processing

getTaxonId() - Method in class io.seqware.webservice.generated.model.Sample

getTemplate() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field template.

getTemplate() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field template.

getTemplateEmail() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams

Getter for the field templateEmail.

getTemplatePath() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field templatePath.

getTemplateType() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Getter for the field templateType.

getTest() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

getTestCmd() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field testCmd.

getTests() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow

getThreads() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

getThreads() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

getThreads() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

getTimeTaken() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Getter for the field timeTaken.

getTissSource() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Getter for the field tissSource.

getTissueOrigin() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Get the value of tissueOrigin

getTissuePreparation() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Get the value of tissuePreparation

getTissueType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Get the value of tissueType

getTitle() - Method in class io.seqware.webservice.generated.model.Experiment

getTitle() - Method in class io.seqware.webservice.generated.model.Sample

getTitle() - Method in class io.seqware.webservice.generated.model.Study

getTitle() - Method in enum net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header

getTitle() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field title.

getTitle() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field title.

getTitle() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field title.

getTotal() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid

Getter for the field total.

getTotalPrice() - Method in class io.seqware.webservice.generated.model.Expense

getTotalPrice() - Method in class net.sourceforge.seqware.common.model.Expense

Getter for the field totalPrice.

getTotalPriceString() - Method in class net.sourceforge.seqware.common.model.Expense

Getter for the field totalPrice.

getTotalUnits() - Method in class io.seqware.webservice.generated.model.Expense

getTotalUnits() - Method in class net.sourceforge.seqware.common.model.Expense

Getter for the field totalUnits.

getType() - Method in class io.seqware.webservice.generated.model.File

getType() - Method in class io.seqware.webservice.generated.model.Lane

getType() - Method in class io.seqware.webservice.generated.model.Sample

getType() - Method in class io.seqware.webservice.generated.model.WorkflowParam

getType() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

getType() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field type.

getType() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field type.

getType() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field type.

getType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Getter for the field type.

getType() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

Getter for the field type.

getType() - Method in class net.sourceforge.seqware.common.module.FileMetadata

getType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement

getType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

getType() - Method in class net.sourceforge.seqware.webservice.dto.FileDto

Getter for the field type.

getType() - Method in class net.sourceforge.solexatools.webapp.controller.SearchController

Getter for the field type.

getTypeNode() - Method in class net.sourceforge.seqware.common.business.UploadFile

Getter for the field typeNode.

getUids(NamingEnumeration<SearchResult>) - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication

getUids.

getUniqueDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

return the unqiue dir associate with the file if the file type is input, the provisioned file will be output to provisionfiles/uniquedir + filename

getUnit() - Method in class io.seqware.webservice.generated.model.FileAttribute

getUnit() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute

getUnit() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute

getUnit() - Method in interface net.sourceforge.seqware.common.model.Attribute

getUnit.

getUnit() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

getUnit() - Method in class net.sourceforge.seqware.common.model.FileAttribute

getUnit.

getUnit() - Method in class net.sourceforge.seqware.common.model.IUSAttribute

getUnit.

getUnit() - Method in class net.sourceforge.seqware.common.model.LaneAttribute

getUnit() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

getUnit.

getUnit() - Method in class net.sourceforge.seqware.common.model.SampleAttribute

getUnit.

getUnit() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute

getUnit.

getUnit() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

getUnit.

getUnit() - Method in class net.sourceforge.seqware.common.model.StudyAttribute

getUnit.

getUnit() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute

getUnit.

getUnit() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute

getUnit.

getUnit() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit

getUnit() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto

Getter for the field unit.

getUnits() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute

getUnits() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute

getUnits() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute

getUnits() - Method in class io.seqware.webservice.generated.model.IusAttribute

getUnits() - Method in class io.seqware.webservice.generated.model.LaneAttribute

getUnits() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute

getUnits() - Method in class io.seqware.webservice.generated.model.SampleAttribute

getUnits() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute

getUnits() - Method in class io.seqware.webservice.generated.model.StudyAttribute

getUnits() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

Getter for the field units.

getUnits() - Method in class net.sourceforge.seqware.common.model.IUSAttribute

Getter for the field units.

getUnits() - Method in class net.sourceforge.seqware.common.model.LaneAttribute

Getter for the field units.

getUnits() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

Getter for the field units.

getUnits() - Method in class net.sourceforge.seqware.common.model.SampleAttribute

Getter for the field units.

getUnits() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

Getter for the field units.

getUnits() - Method in class net.sourceforge.seqware.common.model.StudyAttribute

Getter for the field units.

getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Experiment

Getter for the field updateTimestamp.

getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field updateTimestamp.

getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field updateTimestamp.

getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field updateTimestamp.

getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Registration

Getter for the field updateTimestamp.

getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Sample

Getter for the field updateTimestamp.

getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field updateTimestamp.

getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field updateTimestamp.

getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareStudy

Getter for the field updateTimestamp.

getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

Getter for the field updateTimestamp.

getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Study

Getter for the field updateTimestamp.

getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field updateTimestamp.

getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field updateTimestamp.

getUpdateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Getter for the field updateTimeStamp.

getUpdateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Getter for the field updateTimeStamp.

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Experiment

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Ius

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Lane

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Processing

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Sample

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.SequencerRun

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareExperiment

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareFile

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareLane

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareProcessing

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareSample

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareStudy

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Study

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Workflow

getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareExperiment

Getter for the field updateTstmp.

getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareFile

Getter for the field updateTstmp.

getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareLane

Getter for the field updateTstmp.

getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareProcessing

Getter for the field updateTstmp.

getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareSample

Getter for the field updateTstmp.

getUpdateValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Getter for the field updateValidator.

getUpdateValidator() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

getUpdateValidator.

getUrl() - Method in class io.seqware.webservice.generated.model.ExperimentLink

getUrl() - Method in class io.seqware.webservice.generated.model.File

getUrl() - Method in class io.seqware.webservice.generated.model.IusLink

getUrl() - Method in class io.seqware.webservice.generated.model.LaneLink

getUrl() - Method in class io.seqware.webservice.generated.model.Processing

getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingIus

getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingLanes

getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingSamples

getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingStudies

getUrl() - Method in class io.seqware.webservice.generated.model.SampleLink

getUrl() - Method in class io.seqware.webservice.generated.model.StudyLink

getUrl() - Method in class net.sourceforge.seqware.common.model.ExperimentLink

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.common.model.IUSLink

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.common.model.LaneLink

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingIus

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.common.model.SampleLink

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.common.model.StudyLink

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.common.module.FileMetadata

getUrl() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.webservice.dto.FileDto

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Getter for the field url.

getUrl() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto

Getter for the field url.

getUrlLabel() - Method in class io.seqware.webservice.generated.model.File

getUrlLabel() - Method in class io.seqware.webservice.generated.model.Processing

getUrlLabel() - Method in class net.sourceforge.seqware.common.model.File

Getter for the field urlLabel.

getUrlLabel() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field urlLabel.

getUrlLabel() - Method in class net.sourceforge.seqware.common.module.FileMetadata

getUrlLabel() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field urlLabel.

getUseIparIntensities() - Method in class io.seqware.webservice.generated.model.SequencerRun

getUseIparIntensities() - Method in class net.sourceforge.seqware.common.model.SequencerRun

Getter for the field useIparIntensities.

getUseIparIntensities() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Getter for the field useIparIntensities.

getUseOneURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field useOneURL.

getUserMl() - Method in class io.seqware.webservice.generated.model.Registration

getUsername() - Method in class io.seqware.webservice.generated.model.Workflow

getUsername() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getUsername() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field username.

getUserName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field userName.

getUseTwoURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence

Getter for the field useTwoURL.

getUseURL() - Method in class net.sourceforge.seqware.common.business.UploadFile

Getter for the field useURL.

getValidationReportService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field validationReportService.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Getter for the field validator.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.FileController

Getter for the field validator.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController

Getter for the field validator.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController

Getter for the field validator.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController

Getter for the field validator.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController

Getter for the field validator.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController

Getter for the field validator.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO

Getter for the field validator.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

getValidator.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Getter for the field validator.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Getter for the field validator.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController

Getter for the field validator.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController

Getter for the field validator.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController

Getter for the field validator.

getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController

Getter for the field validator.

getValue() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute

getValue() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute

getValue() - Method in class io.seqware.webservice.generated.model.FileAttribute

getValue() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute

getValue() - Method in class io.seqware.webservice.generated.model.IusAttribute

getValue() - Method in class io.seqware.webservice.generated.model.LaneAttribute

getValue() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute

getValue() - Method in class io.seqware.webservice.generated.model.SampleAttribute

getValue() - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute

getValue() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute

getValue() - Method in class io.seqware.webservice.generated.model.StudyAttribute

getValue() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute

getValue() - Method in class io.seqware.webservice.generated.model.WorkflowParamValue

getValue() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute

getValue() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

getValue() - Method in interface net.sourceforge.seqware.common.model.Attribute

getValue.

getValue() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

Getter for the field value.

getValue() - Method in class net.sourceforge.seqware.common.model.FileAttribute

getValue.

getValue() - Method in class net.sourceforge.seqware.common.model.IUSAttribute

getValue.

getValue() - Method in class net.sourceforge.seqware.common.model.LaneAttribute

Getter for the field value.

getValue() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

getValue.

getValue() - Method in class net.sourceforge.seqware.common.model.SampleAttribute

getValue.

getValue() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute

getValue.

getValue() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

Getter for the field value.

getValue() - Method in class net.sourceforge.seqware.common.model.StudyAttribute

getValue.

getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute

getValue.

getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Getter for the field value.

getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

Getter for the field value.

getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute

getValue.

getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

Getter for the field value.

getValue() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit

getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument

Getter for the field value.

getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile

Getter for the field value.

getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement

getValue() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto

Getter for the field value.

getValues() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Getter for the field values.

getVersion() - Method in class io.seqware.webservice.generated.model.Processing

getVersion() - Method in class io.seqware.webservice.generated.model.Workflow

getVersion() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field version.

getVersion() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field version.

getVersion() - Method in class net.sourceforge.seqware.common.module.ReturnValue

Getter for the field version.

getVersion() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field version.

getVersion() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getVersion() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

getViaAccessions(int[]) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Get the models corresponding to potential accessions

getViaAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getViaAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getViaAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getViaParentAccessions(int[]) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Get the models corresponding to potential parent accessions

getViaParentAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getViaParentAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getViaParentAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getViewName(String) - Static method in class net.sourceforge.solexatools.util.Constant

getViewName.

getVisibleParams() - Method in class net.sourceforge.solexatools.util.SummaryData

Getter for the field visibleParams.

getVisibleWorkflowParams() - Method in class net.sourceforge.seqware.common.model.Workflow

getVisibleWorkflowParams.

getVisibleWorkflowParamsWithDifferentValue() - Method in class net.sourceforge.seqware.common.model.Workflow

getVisibleWorkflowParamsWithDifferentValue.

getWebResource() - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

getWfRuns() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Getter for the field wfRuns.

getWidth() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel

getWorkflow(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Get a workflow

getWorkflow(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflow(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflow(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

Get a workflow

getWorkflow() - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Getter for the field workflow.

getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute

Getter for the field workflow.

getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Getter for the field workflow.

getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field workflow.

getWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getWorkflow_accession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getWorkflow_directory_name() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getWorkflow_engine() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getWorkflow_run_accession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getWorkflowAccession(String, String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getWorkflowAccession.

getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflowAccession.

getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflowAccession.

getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getWorkflowAccession.

getWorkflowAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

getWorkflowAccession() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field workflowAccession.

getWorkflowAccession() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

getWorkflowAccession(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB

getWorkflowAccession.

getWorkflowAccessionsToCheck() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

getWorkflowAttributeCollection() - Method in class io.seqware.webservice.generated.model.Workflow

getWorkflowAttributeId() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute

getWorkflowAttributeId() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute

Getter for the field workflowAttributeId.

getWorkflowAttributes() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field workflowAttributes.

getWorkflowBaseDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getWorkflowBundleDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

getWorkflowBundleDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow

getWorkflowClass() - Method in class io.seqware.webservice.generated.model.Workflow

getWorkflowClass() - Method in class net.sourceforge.seqware.common.model.Workflow

getWorkflowClass() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

getWorkflowCollection() - Method in class io.seqware.webservice.generated.model.Registration

getWorkflowDataModel(Integer, Integer) - Method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowDataModelFactory

load metadata.xml, if FTL, parse the FTL to XML, and translate it to Java based Object if Java, load the class.

getWorkflowDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Getter for the field workflowDir.

getWorkflowEngine() - Method in class io.seqware.webservice.generated.model.Workflow

getWorkflowEngine() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getWorkflowEngine() - Method in class net.sourceforge.seqware.common.model.Workflow

getWorkflowEngine() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

getWorkflowEngine() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

getWorkflowEngine(AbstractWorkflowDataModel, Map<String, String>) - Static method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

getWorkflowId() - Method in class io.seqware.webservice.generated.model.SampleReport

getWorkflowId() - Method in class io.seqware.webservice.generated.model.Workflow

getWorkflowId() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute

getWorkflowId() - Method in class io.seqware.webservice.generated.model.WorkflowParam

getWorkflowId() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getWorkflowId() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field workflowId.

getWorkflowInfo() - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo

getWorkflowInfo.

getWorkflowMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB

getWorkflowMetadata.

getWorkflowParam() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

Getter for the field workflowParam.

getWorkflowParamCollection() - Method in class io.seqware.webservice.generated.model.Workflow

getWorkflowParamId() - Method in class io.seqware.webservice.generated.model.WorkflowParam

getWorkflowParamId() - Method in class io.seqware.webservice.generated.model.WorkflowParamValue

getWorkflowParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Getter for the field workflowParamId.

getWorkflowParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

Getter for the field workflowParamId.

getWorkflowParamMetadata(Integer) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB

getWorkflowParamMetadata.

getWorkflowParams(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getWorkflowParams.

getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflowParams.

getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflowParams.

getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getWorkflowParams.

getWorkflowParams() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field workflowParams.

getWorkflowParamService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field workflowParamService.

getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController

Getter for the field workflowParamService.

getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController

Getter for the field workflowParamService.

getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController

Getter for the field workflowParamService.

getWorkflowParamServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getWorkflowParamServiceBean.

getWorkflowParamsWithDifferentFileMetaType() - Method in class net.sourceforge.seqware.common.model.Workflow

getWorkflowParamsWithDifferentFileMetaType.

getWorkflowParamValueCollection() - Method in class io.seqware.webservice.generated.model.WorkflowParam

getWorkflowParamValueId() - Method in class io.seqware.webservice.generated.model.WorkflowParamValue

getWorkflowParamValueId() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

Getter for the field workflowParamValueId.

getWorkflowParamValueService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field workflowParamValueService.

getWorkflowParamValueService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController

Getter for the field workflowParamValueService.

getWorkflowParamValueService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController

Getter for the field workflowParamValueService.

getWorkflowParamValueServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getWorkflowParamValueServiceBean.

getWorkflowRun() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Getter for the field workflowRun.

getWorkflowRun(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getWorkflowRun.

getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflowRun.

getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflowRun.

getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getWorkflowRun.

getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.Expense

Getter for the field workflowRun.

getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field workflowRun.

getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute

Getter for the field workflowRun.

getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

Getter for the field workflowRun.

getWorkflowRunAccession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

getWorkflowRunAccession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

getWorkflowRunAttributeCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getWorkflowRunAttributeId() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute

getWorkflowRunAttributeId() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute

Getter for the field workflowRunAttributeId.

getWorkflowRunAttributes() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field workflowRunAttributes.

getWorkflowRunByAncestorWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field workflowRunByAncestorWorkflowRunId.

getWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.File

getWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.Registration

getWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.Workflow

getWorkflowRunHtml(WorkflowRun, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil

getWorkflowRunHtml.

getWorkflowRunHtmlWithIUSs(WorkflowRun, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil

getWorkflowRunHtmlWithIUSs.

getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.Expense

getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns

getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns

getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.Processing

getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute

getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.Processing

Getter for the field workflowRunId.

getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

Getter for the field workflowRunId.

getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field workflowRunId.

getWorkflowRunInfo(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB

getWorkflowRunInfo.

getWorkflowRunParam(SortedSet<WorkflowParam>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

getWorkflowRunParam.

getWorkflowRunParamCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getWorkflowRunParamId() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

getWorkflowRunParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

getWorkflowRunParamId.

getWorkflowRunParams() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Getter for the field workflowRunParams.

getWorkflowRunProcessings() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Getter for the field workflowRunProcessings.

getWorkflowRunReport(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getWorkflowRunReport.

getWorkflowRunReport(int, Date, Date) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getWorkflowRunReport.

getWorkflowRunReport(Date, Date) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getWorkflowRunReport.

getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflowRunReport.

getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflowRunReport.

getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflowRunReport.

getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflowRunReport.

getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflowRunReport.

getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflowRunReport.

getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getWorkflowRunReport.

getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getWorkflowRunReport.

getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getWorkflowRunReport.

getWorkflowRunReportStdErr(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getWorkflowRunReportStdErr.

getWorkflowRunReportStdErr(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflowRunReportStdErr(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflowRunReportStdErr(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getWorkflowRunReportStdErr.

getWorkflowRunReportStdOut(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getWorkflowRunReportStdOut.

getWorkflowRunReportStdOut(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflowRunReportStdOut(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflowRunReportStdOut(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getWorkflowRunReportStdOut.

getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.IUS

Getter for the field workflowRuns.

getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.Lane

Getter for the field workflowRuns.

getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.Workflow

Getter for the field workflowRuns.

getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Returns the workflow_runs associated with a group of files.

getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getWorkflowRunsAssociatedWithInputFiles(List<Integer>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Returns the workflow_runs associated with a group of input files.

getWorkflowRunsAssociatedWithInputFiles(List<Integer>, List<Integer>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

Returns the workflow_runs associated with a group of input files.

getWorkflowRunsAssociatedWithInputFiles(List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflowRunsAssociatedWithInputFiles(List<Integer>, List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflowRunsAssociatedWithInputFiles(List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflowRunsAssociatedWithInputFiles(List<Integer>, List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflowRunsAssociatedWithInputFiles(List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getWorkflowRunsAssociatedWithInputFiles(List<Integer>, List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getWorkflowRunsByHost(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getWorkflowRunsByHost.

getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflowRunsByHost.

getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflowRunsByHost.

getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getWorkflowRunsByHost.

getWorkflowRunsByStatus(WorkflowRunStatus) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getWorkflowRunsByStatus.

getWorkflowRunsByStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflowRunsByStatus.

getWorkflowRunsByStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflowRunsByStatus.

getWorkflowRunsByStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getWorkflowRunsByStatus.

getWorkflowRunService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.RetryAnalysisWorkflowController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController

Getter for the field workflowRunService.

getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController

Getter for the field workflowRunService.

getWorkflowRunServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getWorkflowRunServiceBean.

getWorkflowRunWithWorkflow(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

getWorkflowRunWithWorkflow.

getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

getWorkflowRunWithWorkflow.

getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

getWorkflowRunWithWorkflow.

getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

getWorkflowRunWithWorkflow.

getWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

getWorkflows.

getWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

getWorkflows.

getWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

getWorkflows.

getWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

getWorkflows.

getWorkflowsAndRuns() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

getWorkflowService() - Method in class net.sourceforge.seqware.common.ContextImpl

Getter for the field workflowService.

getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController

Getter for the field workflowService.

getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController

Getter for the field workflowService.

getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails

Getter for the field workflowService.

getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController

Getter for the field workflowService.

getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController

Getter for the field workflowService.

getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController

Getter for the field workflowService.

getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController

Getter for the field workflowService.

getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController

Getter for the field workflowService.

getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController

Getter for the field workflowService.

getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController

Getter for the field workflowService.

getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController

Getter for the field workflowService.

getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController

Getter for the field workflowService.

getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController

Getter for the field workflowService.

getWorkflowServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory

getWorkflowServiceBean.

getWorkflowsForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

getWorkflowsForStudy.

getWorkflowsForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService

getWorkflowsForStudy.

getWorkflowsForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

getWorkflowsForStudy.

getWorkflowsForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO

getWorkflowsForStudy.

getWorkflowSqwVersion() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

getWorkflowSqwVersion.

getWorkflowsRun() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems

getWorkflowsRun.

getWorkflowState(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools

This method examines a Pegasus log directory using the status command provided and will encode the state of the workflow in the ReturnValue object, running as ReturnValue.PROCESSING, failed as ReturnValue.FAILURE, and success as ReturnValue.SUCCESS.

getWorkflowTemplate() - Method in class io.seqware.webservice.generated.model.Workflow

getWorkflowTemplate() - Method in class io.seqware.webservice.generated.model.WorkflowRun

getWorkflowType() - Method in class io.seqware.webservice.generated.model.Workflow

getWorkflowType() - Method in class net.sourceforge.seqware.common.model.Workflow

getWorkflowType() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

getWorkflowType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of workflowType

getWorkingDirectory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine

The working directory for the prepared workflow run, or null if not yet prepared or if not applicable for the concrete engine.

getWorkingDirectory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine

getWorkingDirectory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine

getWS(Map<String, String>) - Static method in class net.sourceforge.seqware.common.metadata.MetadataFactory

getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.ExperimentIDFilter

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.IUSIDFilter

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.LaneIDFilter

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentLibraryDesignResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentSpotDesignReadSpecResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentSpotDesignResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileIDResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusIDResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneIDResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySelectionResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySourceResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryStrategyResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.OrganismResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.PlatformResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.RootSampleResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource

getXml.

getXML() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource

getXML.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyTypeResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource

getXml.

getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource

getXml.

givesPermission(Registration) - Method in class net.sourceforge.seqware.common.security.PermissionsAware

givesPermission(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.security.PermissionsAware

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Expense

Short-circuit permission checking by providing a set of entities that have already been checked

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Experiment

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.File

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Invoice

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.IUS

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Lane

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Processing

Short-circuit permission checking by providing a set of entities that have already been checked

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Registration

Short-circuit permission checking by providing a set of entities that have already been checked

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Sample

Short-circuit permission checking by providing a set of entities that have already been checked

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Short-circuit permission checking by providing a set of entities that have already been checked

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Study

Short-circuit permission checking by providing a set of entities that have already been checked

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Workflow

Short-circuit permission checking by providing a set of entities that have already been checked

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Short-circuit permission checking by providing a set of entities that have already been checked

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

Short-circuit permission checking by providing a set of entities that have already been checked

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Short-circuit permission checking by providing a set of entities that have already been checked

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

Short-circuit permission checking by providing a set of entities that have already been checked

givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.security.PermissionsAware

Short-circuit permission checking by providing a set of entities that have already been checked

gridProxyInit() - Static method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

H

handle(ResultSet) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB.IntByIndex

handle(ResultSet) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB.IntByName

handle(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect

handle(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion.OptionalSlashRedirect

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.CycleCheckResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.FileProvenanceResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.GenericDBResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.ProcessIdProcessResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.RunWorkflowResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.SampleHierarchyResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.SampleIdFilesResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.SequencerRunIdFilesResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.SequencerRunReportResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesTSVResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.TriggerFileProvenanceResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowReportResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIdFilesResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDProcessingsResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDWorkflowResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRuntimeResource

handle(ResultSet) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource.IntListByName

handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessingStructureResource

handle(Callback[]) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos.NamePasswordCallbackHandler

handleCancel(HttpServletRequest, HttpServletResponse, WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController

Handles the user's request to delete their study.

handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Handles the user's request to cancel the study or the study update page.

handleCancel(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController

Handles the user's request to cancel the lane or the lane update page.

handleCancel(HttpServletRequest, HttpServletResponse, IUS) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController

Handles the user's request to cancel.

handleCancel(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController

Handles the user's request to cancel the lane or the lane update page.

handleCancel(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController

Handles the user's request to cancel the sequencerRun or the sequencerRun update page.

handleCancel(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController

Handles the user's request to cancel the registration or the registration update page.

handleCancel(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController

Handles the user's request to cancel the study or the study update page.

handleCancel(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController

Handles the user's request to cancel the experiment or the experiment update page.

handleCancel(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO

Handles the user's request to cancel the experiment or the experiment update page.

handleCancel(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Handles the user's request to cancel the registration or the registration update page.

handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

Handles the user's request to cancel the study or the study update page.

handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController

Handles the user's request to cancel the study or the study update page.

handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Handles the user's request to cancel the study or the study update page.

handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Handles the user's request to cancel the study or the study update page.

handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController

Handles the user's request to cancel the study or the study update page.

handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController

Handles the user's request to cancel the study or the study update page.

handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController

Handles the user's request to cancel the study or the study update page.

handleCancel(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController

Handles the user's request to cancel the registration or the registration update page.

handleDelete(HttpServletRequest, HttpServletResponse, WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController

Handles the user's request to delete their study.

handleDelete(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Handles the user's request to delete their experiment.

handleDelete(HttpServletRequest, HttpServletResponse, File) - Method in class net.sourceforge.solexatools.webapp.controller.FileController

Handles the user's request to delete their file.

handleDelete(HttpServletRequest, HttpServletResponse, IUS) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController

Handles the user's request to delete their ius.

handleDelete(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController

Handles the user's request to delete their lane.

handleDelete(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController

Handles the user's request to delete their processing.

handleDelete(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController

Handles the user's request to delete their sample.

handleDelete(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Handles the user's request to delete their study.

handleDelete(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

Handles the user's request to delete their study.

handleDelete(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController

Handles the user's request to delete their study.

handleDelete(HttpServletRequest, HttpServletResponse, WorkflowParam) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController

Handles the user's request to delete their study.

handleDelete(HttpServletRequest, HttpServletResponse, WorkflowParamValue) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController

Handles the user's request to delete their study.

handleGroupByAttribute(String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

handleNext(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController

Handles the user's request to submit a new study.

handleNext(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController

Handles the user's request to submit a new study.

handlePrevious(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController

Handles the user's request to cancel the study or the study update page.

handlePrevious(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController

Handles the user's request to cancel the study or the study update page.

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AbortLoadIndexPageController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderSizeValidatorController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.CancelBulkDownloaderController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.CancelInputDownloaderController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LogoutController

Handles a user's logout request.

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.RetryAnalysisWorkflowController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyTableController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyTableControllerDetails

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController

handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController

handleReset(HttpServletRequest, HttpServletResponse, Experiment) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Handles the user's request to reset the experiment page during a new or update experiment.

handleReset(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController

Handles the user's request to reset the lane page during a new or update lane.

handleReset(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController

Handles the user's request to reset the lane page during a new or update lane.

handleReset(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController

Handles the user's request to reset the sequencerRun page during a new or update sequencerRun.

handleReset(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController

Handles the user's request to reset the registration page during a new or update registration.

handleReset(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController

Handles the user's request to reset the sample page during a new or update sample.

handleReset(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController

Handles the user's request to reset the experiment page during a new or update experiment.

handleReset(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO

Handles the user's request to reset the experiment page during a new or update experiment.

handleReset(HttpServletRequest, HttpServletResponse, SequencerRunWizardDTO) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Handles the user's request to reset the registration page during a new or update registration.

handleReset(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

Handles the user's request to reset the study page during a new or update study.

handleReset(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController

Handles the user's request to reset the study page during a new or update study.

handleReset(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController

Handles the user's request to reset the study page during a new or update study.

handleReset(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController

Handles the user's request to reset the study page during a new or update study.

handleReset(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController

Handles the user's request to reset the registration page during a new or update registration.

handleShare(HttpServletRequest, HttpServletResponse, WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController

Handles the user's request to share their WorkflowRun.

handleShare(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

Handles the user's request to share their study.

handleShare(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController

Handles the user's request to share their study.

handleSubmit(HttpServletRequest, HttpServletResponse, Experiment) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Handles the user's request to submit a new study.

handleSubmit(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController

Handles the user's request to submit a new lane.

handleSubmit(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController

Handles the user's request to submit a new lane.

handleSubmit(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController

Handles the user's request to submit a new sequencerRun.

handleSubmit(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController

Handles the user's request to submit a new registration.

handleSubmit(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController

Handles the user's request to submit a new study.

handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController

Handles the user's request to submit a new experiment.

handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO

Handles the user's request to submit a new experiment.

handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRunWizardDTO) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Handles the user's request to submit a new registration.

handleSubmit(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

Handles the user's request to submit a new study.

handleSubmit(HttpServletRequest, HttpServletResponse, UploadFile) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Handles the user's request to submit a new study.

handleSubmit(HttpServletRequest, HttpServletResponse, UploadSequence) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Handles the user's request to submit a new study.

handleSubmit(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController

Handles the user's request to submit a new study.

handleSubmit(HttpServletRequest, HttpServletResponse, WorkflowParam) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController

Handles the user's request to submit a new study.

handleSubmit(HttpServletRequest, HttpServletResponse, WorkflowParamValue) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController

Handles the user's request to submit a new study.

handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRunWizardDTO) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController

Handles the user's request to submit a new registration.

handleUpdate(HttpServletRequest, HttpServletResponse, Experiment) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Handles the user's request to update their study.

handleUpdate(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController

Handles the user's request to update their lane.

handleUpdate(HttpServletRequest, HttpServletResponse, IUS) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController

Handles the user's request to delete their ius.

handleUpdate(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController

Handles the user's request to update their lane.

handleUpdate(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController

Handles the user's request to update their sequencerRun.

handleUpdate(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController

Handles the user's request to update their registration.

handleUpdate(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController

Handles the user's request to update their study.

handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController

Handles the user's request to update their experiment.

handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO

Handles the user's request to update their experiment.

handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Handles the user's request to update their registration.

handleUpdate(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

Handles the user's request to update their study.

handleUpdate(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController

Handles the user's request to update their study.

handleUpdate(HttpServletRequest, HttpServletResponse, WorkflowParam) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController

Handles the user's request to update their study.

handleUpdate(HttpServletRequest, HttpServletResponse, WorkflowParamValue) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController

Handles the user's request to update their study.

handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController

Handles the user's request to update their registration.

handleWorkflowRunsViaChild(Set<File>, Hibernate3DtoCopier) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource

handleWorkflowRunsViaIUS(Set<File>, Hibernate3DtoCopier) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource

handleWorkflowRunsViaLane(Set<File>, Hibernate3DtoCopier) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource

hasEmailAddressBeenUsed(String) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl

hasEmailAddressBeenUsed.

hasEmailAddressBeenUsed(String) - Method in interface net.sourceforge.seqware.common.business.RegistrationService

hasEmailAddressBeenUsed.

hasFork() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

hashCode() - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple

hashCode() - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple

hashCode() - Method in class io.seqware.webservice.generated.model.Expense

hashCode() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute

hashCode() - Method in class io.seqware.webservice.generated.model.Experiment

hashCode() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute

hashCode() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

hashCode() - Method in class io.seqware.webservice.generated.model.ExperimentLink

hashCode() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

hashCode() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

hashCode() - Method in class io.seqware.webservice.generated.model.File

hashCode() - Method in class io.seqware.webservice.generated.model.FileAttribute

hashCode() - Method in class io.seqware.webservice.generated.model.FileReport

hashCode() - Method in class io.seqware.webservice.generated.model.FileType

hashCode() - Method in class io.seqware.webservice.generated.model.Invoice

hashCode() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute

hashCode() - Method in class io.seqware.webservice.generated.model.Ius

hashCode() - Method in class io.seqware.webservice.generated.model.IusAttribute

hashCode() - Method in class io.seqware.webservice.generated.model.IusLink

hashCode() - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns

hashCode() - Method in class io.seqware.webservice.generated.model.Lane

hashCode() - Method in class io.seqware.webservice.generated.model.LaneAttribute

hashCode() - Method in class io.seqware.webservice.generated.model.LaneLink

hashCode() - Method in class io.seqware.webservice.generated.model.LaneType

hashCode() - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns

hashCode() - Method in class io.seqware.webservice.generated.model.LibrarySelection

hashCode() - Method in class io.seqware.webservice.generated.model.LibrarySource

hashCode() - Method in class io.seqware.webservice.generated.model.LibraryStrategy

hashCode() - Method in class io.seqware.webservice.generated.model.Organism

hashCode() - Method in class io.seqware.webservice.generated.model.Platform

hashCode() - Method in class io.seqware.webservice.generated.model.Processing

hashCode() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute

hashCode() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

hashCode() - Method in class io.seqware.webservice.generated.model.ProcessingFiles

hashCode() - Method in class io.seqware.webservice.generated.model.ProcessingIus

hashCode() - Method in class io.seqware.webservice.generated.model.ProcessingLanes

hashCode() - Method in class io.seqware.webservice.generated.model.ProcessingRelationship

hashCode() - Method in class io.seqware.webservice.generated.model.ProcessingSamples

hashCode() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

hashCode() - Method in class io.seqware.webservice.generated.model.ProcessingStudies

hashCode() - Method in class io.seqware.webservice.generated.model.Registration

hashCode() - Method in class io.seqware.webservice.generated.model.Sample

hashCode() - Method in class io.seqware.webservice.generated.model.SampleAttribute

hashCode() - Method in class io.seqware.webservice.generated.model.SampleLink

hashCode() - Method in class io.seqware.webservice.generated.model.SampleRelationship

hashCode() - Method in class io.seqware.webservice.generated.model.SampleReport

hashCode() - Method in class io.seqware.webservice.generated.model.SampleSearch

hashCode() - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute

hashCode() - Method in class io.seqware.webservice.generated.model.SequencerRun

hashCode() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute

hashCode() - Method in class io.seqware.webservice.generated.model.ShareExperiment

hashCode() - Method in class io.seqware.webservice.generated.model.ShareFile

hashCode() - Method in class io.seqware.webservice.generated.model.ShareLane

hashCode() - Method in class io.seqware.webservice.generated.model.ShareProcessing

hashCode() - Method in class io.seqware.webservice.generated.model.ShareSample

hashCode() - Method in class io.seqware.webservice.generated.model.ShareStudy

hashCode() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

hashCode() - Method in class io.seqware.webservice.generated.model.Study

hashCode() - Method in class io.seqware.webservice.generated.model.StudyAttribute

hashCode() - Method in class io.seqware.webservice.generated.model.StudyLink

hashCode() - Method in class io.seqware.webservice.generated.model.StudyType

hashCode() - Method in class io.seqware.webservice.generated.model.Workflow

hashCode() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute

hashCode() - Method in class io.seqware.webservice.generated.model.WorkflowParam

hashCode() - Method in class io.seqware.webservice.generated.model.WorkflowParamValue

hashCode() - Method in class io.seqware.webservice.generated.model.WorkflowRun

hashCode() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute

hashCode() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

hashCode() - Method in class net.sourceforge.seqware.common.model.Expense

hashCode() - Method in class net.sourceforge.seqware.common.model.Experiment

hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

hashCode.

hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

hashCode.

hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

hashCode() - Method in class net.sourceforge.seqware.common.model.File

hashCode() - Method in class net.sourceforge.seqware.common.model.FileType

hashCode() - Method in class net.sourceforge.seqware.common.model.Invoice

hashCode() - Method in class net.sourceforge.seqware.common.model.IUS

hashCode() - Method in class net.sourceforge.seqware.common.model.Lane

hashCode() - Method in class net.sourceforge.seqware.common.model.LibrarySelection

hashCode() - Method in class net.sourceforge.seqware.common.model.LibrarySource

hashCode() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy

hashCode() - Method in class net.sourceforge.seqware.common.model.Organism

hashCode.

hashCode() - Method in class net.sourceforge.seqware.common.model.Platform

hashCode() - Method in class net.sourceforge.seqware.common.model.Processing

hashCode() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

hashCode() - Method in class net.sourceforge.seqware.common.model.Registration

hashCode.

hashCode() - Method in class net.sourceforge.seqware.common.model.Sample

hashCode() - Method in class net.sourceforge.seqware.common.model.SampleAttribute

hashCode() - Method in class net.sourceforge.seqware.common.model.SequencerRun

hashCode() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

hashCode() - Method in class net.sourceforge.seqware.common.model.ShareStudy

hashCode() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

hashCode() - Method in class net.sourceforge.seqware.common.model.Study

hashCode() - Method in class net.sourceforge.seqware.common.model.StudyAttribute

hashCode() - Method in class net.sourceforge.seqware.common.model.StudyType

hashCode() - Method in class net.sourceforge.seqware.common.model.Workflow

hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

hashCode.

hashCode() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument

hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

hasJoin() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

hasMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

hasMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

hasMetadataWriteback - Variable in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

hasMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

hasMetadataWriteback() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

job specific metadata is not supported yet

hasMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

hasNameBeenUsed.

hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

hasNameBeenUsed.

hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

hasNameBeenUsed.

hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.LaneService

hasNameBeenUsed.

hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.SampleService

hasNameBeenUsed.

hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

hasNameBeenUsed.

hasProperty(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

hasPropertyAndNotNull(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

hasRequiredValues() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

hasTitleBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

hasTitleBeenUsed.

hasTitleBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

hasTitleBeenUsed.

hasTitleBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

hasTitleBeenUsed.

hasTitleBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.StudyService

hasTitleBeenUsed.

hasVariable(String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.StringUtils

check if a string has FTL style variables ${variable}

HDFS_Check - Class in io.seqware.pipeline.plugins.sanity.checks

Checks to ensure that you are connected to hdfs by creating a file and deleting it on exit

HDFS_Check() - Constructor for class io.seqware.pipeline.plugins.sanity.checks.HDFS_Check

hello(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.SequencerRunIdFilesResource

hello.

hello(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesResource

hello.

hello(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIdFilesResource

hello.

HelloWorld - Class in net.sourceforge.seqware.pipeline.plugins

HelloWorld class.

HelloWorld() - Constructor for class net.sourceforge.seqware.pipeline.plugins.HelloWorld

Constructor for HelloWorld.

hibernateCalls() - Method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions

hibernateCalls.

HOST - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

hostname - Variable in class net.sourceforge.seqware.common.util.filetools.FileTools.LocalhostPair

HTMLTagValidator - Class in net.sourceforge.solexatools.util

HTMLTagValidator class.

HTMLTagValidator() - Constructor for class net.sourceforge.solexatools.util.HTMLTagValidator

Constructor for HTMLTagValidator.

human_str - Variable in enum net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility.HumanProvenanceFilters

I

info(Object) - Static method in class net.sourceforge.seqware.common.util.Log

See Category.info(Object).

info(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log

See Category.info(Object,Throwable).

ini2Map(String, Map<String, String>) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools

ini2Map.

ini2Map(String, Map<String, String>, boolean) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools

ini2Map.

ini2Map(InputStream, Map<String, String>, boolean) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools

ini2Map.

ini2RichMap(String, Map<String, Map<String, String>>) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools

This is a little different than the ini2Map since it allows us to read ini files where key-value annotations on the key-values appear in comments on the previous line above the current such as: key=bam_inputs:type=file:display=T:display_name=BAM Input(s):file_meta_type=application/bam or key=run_ends:type=pulldown:display=T:display_name=Single or Paired Ends:pulldown_items=Single End|1;Paired End|2 The extra information is used by the Portal and Web Service to display interfaces that let people call the workflows correctly.

iniString2Map(String) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools

iniString2Map.

init() - Method in class io.seqware.pipeline.plugins.sanity.SanityCheck

Plugin initialization code goes here.

init() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

init() - Method in class net.sourceforge.seqware.pipeline.module.Module

init.

init() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface

Module initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner

init.

init() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver

Deprecated.

init.

init() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

init.

init() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

init.

init() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

init.

init() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

init() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugins.deletion.DeletionDB

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker

init() - Method in class net.sourceforge.seqware.pipeline.plugins.fileprovenance.FileProvenanceReporter

init() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot

init() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot

init() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter

Plugin initialization code goes here.

init() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker

Plugin initialization code goes here.

init(Request) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet

init.

initBinder(HttpServletRequest, ServletRequestDataBinder) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

initConf(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine

initHdfsWorkDir(AbstractWorkflowDataModel, Configuration, File) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine

initNfsWorkDir(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine

INPUT_FILE_FILE_PATHS - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

INPUT_FILE_META_TYPES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

INPUT_FILE_SWIDS - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

INPUT_FILES - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

inputFile - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

inputSize - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

insert(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService

insert.

insert(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

insert.

insert(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

insert.

insert(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService

insert.

insert(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService

insert.

insert(File) - Method in interface net.sourceforge.seqware.common.business.FileService

insert.

insert(Registration, File) - Method in interface net.sourceforge.seqware.common.business.FileService

insert.

insert(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl

insert.

insert(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

insert.

insert(Registration, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

insert.

insert(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl

insert.

insert(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl

insert.

insert(File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

insert.

insert(Registration, File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

insert.

insert(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl

Inserts a new Invoice and returns its sw_accession number.

insert(Registration, Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl

insert.

insert(IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

insert.

insert(Registration, IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

insert.

insert(Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

insert.

insert(Registration, Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

insert.

insert(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl

insert.

insert(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl

insert.

insert(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl

insert.

insert(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl

insert.

insert(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl

insert.

insert(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl

insert.

insert(SequencerRun, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

insert.

insert(Registration, SequencerRun, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

insert.

insert(Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

Inserts a new Processing and returns its sw_accession number.

insert(Registration, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

insert.

insert(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl

insert.

insert(RegistrationDTO) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl

insert.

insert(String[], InvitationParams, MailSender) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl

insert.

insert(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

insert.

insert(Registration, Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

insert.

insert(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

insert.

insert(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

This is being used to create a new SequencerRun object and the correct number of assocated Lanes

insert(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

insert.

insert(Registration, SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

insert.

insert(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl

insert.

insert(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl

insert.

insert(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl

insert.

insert(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl

insert.

insert(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl

insert.

insert(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl

insert.

insert(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl

insert.

insert(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

insert.

insert(Registration, Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

insert.

insert(StudyType) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl

insert.

insert(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl

Inserts a new WorkflowParam and returns its primary key.

insert(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl

insert.

insert(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl

Inserts a new WorkflowParamValue and returns its primary key.

insert(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl

insert.

insert(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl

insert.

insert(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl

insert.

insert(WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

Inserts a new WorkflowRun and returns its sw_accession number.

insert(WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

insert.

insert(Registration, WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

insert.

insert(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

insert.

insert(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

Inserts a new Workflow and returns its sw_accession number.

insert(Registration, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

insert.

insert(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService

Inserts a new Invoice and returns its sw_accession number.

insert(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService

insert.

insert(IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService

insert.

insert(Registration, IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService

insert.

insert(Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService

insert.

insert(Registration, Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService

insert.

insert(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService

insert.

insert(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService

insert.

insert(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService

insert.

insert(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService

insert.

insert(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService

insert.

insert(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService

insert.

insert(SequencerRun, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

insert.

insert(Registration, SequencerRun, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

insert.

insert(Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

Inserts a new Processing and returns its sw_accession number.

insert(Registration, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

insert.

insert(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService

insert.

insert(RegistrationDTO) - Method in interface net.sourceforge.seqware.common.business.RegistrationService

insert.

insert(String[], InvitationParams, MailSender) - Method in interface net.sourceforge.seqware.common.business.RegistrationService

insert.

insert(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService

insert.

insert(Registration, Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService

insert.

insert(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

insert.

insert(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

insert.

insert(SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

insert.

insert(Registration, SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

insert.

insert(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService

insert.

insert(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService

insert.

insert(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService

insert.

insert(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService

insert.

insert(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService

insert.

insert(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService

insert.

insert(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService

insert.

insert(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService

insert.

insert(Registration, Study) - Method in interface net.sourceforge.seqware.common.business.StudyService

insert.

insert(StudyType) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService

insert.

insert(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService

Inserts a new WorkflowParam and returns its primary key.

insert(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService

insert.

insert(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService

Inserts a new WorkflowParamValue and returns its primary key.

insert(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService

insert.

insert(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService

insert.

insert(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService

insert.

insert(WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

Inserts a new WorkflowRun and returns its sw_accession number.

insert(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

insert.

insert(WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

insert.

insert(Registration, WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

insert.

insert(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

Inserts a new Workflow and returns its sw_accession number.

insert(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

insert.

insert(ExperimentAttribute) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO

insert.

insert(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

insert.

insert(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

insert.

insert(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO

insert.

insert(ExperimentLink) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO

insert.

insert(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO

insert.

insert(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO

insert.

insert(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

insert.

insert(Registration, File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

insert.

insert(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate

insert.

insert(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

insert.

insert(Registration, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

insert.

insert(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate

insert.

insert(ExperimentLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate

insert.

insert(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate

insert.

insert(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate

insert.

insert(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

insert.

insert(Registration, File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

insert.

insert(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate

Inserts a new Invoice and returns its sw_accession number.

insert(Registration, Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate

insert.

insert(IUSAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate

insert.

insert(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

insert.

insert(Registration, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

insert.

insert(IUSLink) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO

insert.

insert(IUSLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate

insert.

insert(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO

insert.

insert(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate

insert.

insert(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

insert.

insert(Registration, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

insert.

insert(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO

insert.

insert(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate

insert.

insert(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate

insert.

insert(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

Inserts a new Processing and returns its sw_accession number.

insert(Registration, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

insert.

insert(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate

insert.

insert(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate

insert.

insert(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate

insert.

insert(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate

insert.

insert(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate

insert.

insert(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate

insert.

insert(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate

insert.

insert(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate

insert.

insert(SampleAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate

insert.

insert(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

insert.

insert(Registration, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

insert.

insert(SampleLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate

insert.

insert(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

insert.

insert(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

insert.

insert(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

insert.

insert(Registration, SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

insert.

insert(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate

insert.

insert(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate

insert.

insert(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate

insert.

insert(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate

insert.

insert(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate

insert.

insert(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate

insert.

insert(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate

insert.

insert(StudyAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate

insert.

insert(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

insert.

insert(Registration, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

insert.

insert(StudyLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate

insert.

insert(StudyType) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate

insert.

insert(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

Inserts a new Workflow and returns its sw_accession number.

insert(Registration, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

insert.

insert(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate

Inserts a new WorkflowParam and returns its primary key.

insert(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate

insert.

insert(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate

Inserts a new WorkflowParamValue and returns its primary key.

insert(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate

insert.

insert(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

Inserts a new WorkflowRun and returns its sw_accession number.

insert(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

insert.

insert(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate

insert.

insert(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate

insert.

insert(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO

Inserts a new Invoice and returns its sw_accession number.

insert(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO

insert.

insert(IUSAttribute) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO

insert.

insert(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

insert.

insert(Registration, IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

insert.

insert(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

insert.

insert(Registration, Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

insert.

insert(ProcessingAttribute) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO

insert.

insert(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

Inserts a new Processing and returns its sw_accession number.

insert(Registration, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

insert.

insert(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO

insert.

insert(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO

insert.

insert(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO

insert.

insert(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO

insert.

insert(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO

insert.

insert(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO

insert.

insert(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO

insert.

insert(Registration) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO

insert.

insert(SampleAttribute) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO

insert.

insert(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

insert.

insert(Registration, Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

insert.

insert(SampleLink) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO

insert.

insert(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

insert.

insert(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

insert.

insert(SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

insert.

insert(Registration, SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

insert.

insert(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO

insert.

insert(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO

insert.

insert(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO

insert.

insert(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO

insert.

insert(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO

insert.

insert(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO

insert.

insert(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO

insert.

insert(StudyAttribute) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO

insert.

insert(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

insert.

insert(Registration, Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

insert.

insert(StudyLink) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO

insert.

insert(StudyType) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO

insert.

insert(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

Inserts a new Workflow and returns its sw_accession number.

insert(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

insert.

insert(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO

Inserts a new WorkflowParam and returns its primary key.

insert(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO

insert.

insert(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO

Inserts a new WorkflowParamValue and returns its primary key.

insert(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO

insert.

insert(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

Inserts a new WorkflowRun and returns its sw_accession number.

insert(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

insert.

insert(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO

insert.

insert(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO

insert.

InsertAndReturnNewPrimaryKey(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

Find out the primary key for the last inserted record FIXME: This is hardcoded for Postgres, need to make DB agnostic

InsertAndReturnNewPrimaryKey(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

Find out the primary key for the last inserted record FIXME: This is hardcoded for Postgres, need to make DB agnostic

insertFilesAsWorkflowRunParam(WorkflowRun, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate

insertFilesAsWorkflowRunParam.

insertFilesAsWorkflowRunParam(Registration, WorkflowRun, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate

insertFilesAsWorkflowRunParam.

insertFilesAsWorkflowRunParam(WorkflowRun, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO

insertFilesAsWorkflowRunParam.

insertFilesAsWorkflowRunParam(Registration, WorkflowRun, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO

insertFilesAsWorkflowRunParam.

insertLane(Registration, Sample, UploadSequence, FileType) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

insertLane.

insertLane(Registration, Sample, UploadSequence, FileType) - Method in interface net.sourceforge.seqware.common.business.LaneService

insertLane.

insertWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource

insertWorkflowRun.

InSessionExecutions - Class in net.sourceforge.seqware.common.hibernate

Abstract InSessionExecutions class.

InSessionExecutions() - Constructor for class net.sourceforge.seqware.common.hibernate.InSessionExecutions

installBundle(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

installBundle.

installBundle(File, File, boolean, boolean) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

This method allows you to install the workflow bundle to the metadb optionally building a zip file along the way and archiving it to a safe location.

installBundleDirOnly(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

installBundleDirOnly.

installBundleZipOnly(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

installBundleZipOnly.

installHandyProvidedBundle() - Method in class io.seqware.pipeline.plugins.sanity.ProvidedBundleUserPhase5

instance - Static variable in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

instanceOf(Object, String) - Static method in class net.sourceforge.solexatools.util.TagUtils

instanceOf.

IntegerList - Class in net.sourceforge.seqware.common.model.lists

List of integers.

IntegerList() - Constructor for class net.sourceforge.seqware.common.model.lists.IntegerList

Constructor for FileList.

interactive - Variable in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

interactive - Variable in class net.sourceforge.seqware.pipeline.plugins.Metadata

intersection(Set<T>, Set<T>) - Static method in class net.sourceforge.seqware.pipeline.tools.SetOperations

INVALIDARGUMENT - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant INVALIDARGUMENT=9

INVALIDFILE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant INVALIDFILE=7

INVALIDPARAMETERS - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant INVALIDPARAMETERS=2

INVALIDPLUGIN - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant INVALIDPLUGIN=120

InvitationParams - Class in net.sourceforge.seqware.common.invitation

InvitationParams class.

InvitationParams(boolean, String, String) - Constructor for class net.sourceforge.seqware.common.invitation.InvitationParams

Constructor for InvitationParams.

InviteNewUserController - Class in net.sourceforge.solexatools.webapp.controller

InviteNewUserController class.

InviteNewUserController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InviteNewUserController

Constructor for InviteNewUserController.

InviteNewUserSetupController - Class in net.sourceforge.solexatools.webapp.controller

InviteNewUserSetupController class.

InviteNewUserSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InviteNewUserSetupController

Constructor for InviteNewUserSetupController.

InviteNewUserValidatorController - Class in net.sourceforge.solexatools.webapp.controller

InviteNewUserValidatorController class.

InviteNewUserValidatorController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController

Constructor for InviteNewUserValidatorController.

Invoice - Class in io.seqware.webservice.generated.model

Invoice() - Constructor for class io.seqware.webservice.generated.model.Invoice

Invoice(Integer) - Constructor for class io.seqware.webservice.generated.model.Invoice

Invoice(Integer, Date, Date, Date) - Constructor for class io.seqware.webservice.generated.model.Invoice

Invoice - Class in net.sourceforge.seqware.common.model

Invoice class.

Invoice() - Constructor for class net.sourceforge.seqware.common.model.Invoice

Constructor for Invoice.

InvoiceAttribute - Class in io.seqware.webservice.generated.model

InvoiceAttribute() - Constructor for class io.seqware.webservice.generated.model.InvoiceAttribute

InvoiceAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.InvoiceAttribute

InvoiceAttributeFacadeREST - Class in io.seqware.webservice.generated.controller

InvoiceAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.InvoiceAttributeFacadeREST

InvoiceDAO - Interface in net.sourceforge.seqware.common.dao

InvoiceDAO interface.

InvoiceDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

InvoiceDAOHibernate class.

InvoiceDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate

Constructor for InvoiceDAOHibernate.

InvoiceDetailsController - Class in net.sourceforge.solexatools.webapp.controller

InvoiceDetailsController class.

InvoiceDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController

Constructor for InvoiceDetailsController.

InvoiceFacadeREST - Class in io.seqware.webservice.generated.controller

InvoiceFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.InvoiceFacadeREST

InvoiceService - Interface in net.sourceforge.seqware.common.business

InvoiceService interface.

invoiceService - Variable in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController

invoiceService - Variable in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController

InvoiceServiceImpl - Class in net.sourceforge.seqware.common.business.impl

InvoiceServiceImpl class.

InvoiceServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl

Constructor for InvoiceServiceImpl.

InvoiceState - Enum in net.sourceforge.seqware.common.model

io.seqware - package io.seqware

io.seqware.cli - package io.seqware.cli

io.seqware.pipeline.plugins.sanity - package io.seqware.pipeline.plugins.sanity

io.seqware.pipeline.plugins.sanity.checks - package io.seqware.pipeline.plugins.sanity.checks

io.seqware.webservice.adapter - package io.seqware.webservice.adapter

io.seqware.webservice.client - package io.seqware.webservice.client

io.seqware.webservice.controller - package io.seqware.webservice.controller

io.seqware.webservice.generated.client - package io.seqware.webservice.generated.client

io.seqware.webservice.generated.controller - package io.seqware.webservice.generated.controller

io.seqware.webservice.generated.model - package io.seqware.webservice.generated.model

isAttached() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

isAuthenticated(HttpServletRequest) - Static method in class net.sourceforge.solexatools.Security

isAuthenticated.

isCheckEmail(String) - Static method in class net.sourceforge.solexatools.validation.LoginValidator

isCheckEmail.

isConfigError(Throwable) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos

isConfigError.

isCountAsFail(BasicDecider.FILE_STATUS, BasicDecider.PREVIOUS_RUN_STATUS) - Static method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

We now use the guideline that we only count failures when they occur on the same number of files (with the same paths)

isDBTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.BundleDir_Check

isDBTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.CLICheck

isDBTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_Check

isDBTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_WS_ConsistencyCheck

isDBTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.HDFS_Check

isDBTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.Oozie_Check

isDBTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.Script_Check

isDBTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.TutorialCheck

isDBTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.WS_Check

isDBTest() - Method in interface io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface

isDisplay() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

isDisplay.

isDoRerun(BasicDecider.FILE_STATUS, BasicDecider.PREVIOUS_RUN_STATUS) - Static method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

See https://wiki.oicr.on.ca/display/SEQWARE/BasicDecider+logic

isDuplicateFile(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

isDuplicateFile.

isDuplicateFile(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

isDuplicateFile.

isDuplicateFile(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

isDuplicateFile.

isDuplicateFile(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

isDuplicateFile.

isEnd() - Method in class net.sourceforge.solexatools.util.PageInfo

isEnd.

isExists(String, String) - Method in interface net.sourceforge.seqware.common.business.FileService

isExists.

isExists(String, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

isExists.

isExistsShare(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl

isExistsShare.

isExistsShare(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl

isExistsShare.

isExistsShare(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService

isExistsShare.

isExistsShare(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService

isExistsShare.

isFileOwner(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

This tool uses the 'whoami' and 'stat' commands to verify if the current users running this program is the owner for the specified file or directory.

isFinalized() - Method in class net.sourceforge.seqware.common.model.Invoice

isFinalized.

isForceCopy() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

isFullyPaid() - Method in class net.sourceforge.seqware.common.model.Invoice

isFullyPaid.

isGcrSkipIfMissing() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command

isGcrSkipIfOutputExists() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command

isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

isHasFile.

isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

isHasFile.

isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

isHasFile.

isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

isHasFile.

isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

isHasFile.

isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

isHasFile.

isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

isHasFile.

isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

isHasFile.

isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

isHasFile.

isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

isHasFile.

isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

isHasFile.

isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

isHasFile.

isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

isHasFile.

isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

isHasFile.

isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService

isHasFile.

isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.IUSService

isHasFile.

isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService

isHasFile.

isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.LaneService

isHasFile.

isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

isHasFile.

isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService

isHasFile.

isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.SampleService

isHasFile.

isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService

isHasFile.

isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.StudyService

isHasFile.

isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

isHasFile.

isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

isHasFile.

isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

isHasFile.

isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

isHasFile.

isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

isHasFile.

isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

isHasFile.

isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

isHasFile.

isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

isHasFile.

isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

isHasFile.

isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

isHasFile.

isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

isHasFile.

isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

isHasFile.

isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

isHasFile.

isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

isHasFile.

isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

isHasFile.

isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

isHasFile.

isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

isHasFile.

isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

isHasFile.

isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

isHasFile.

isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

isHasFile.

isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

isHasFile.

isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

isHasFile.

isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

isHasFile.

isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

isHasFile.

isInput() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

is an input file?

isInstalled() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

isJoinDevelopersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration

isJoinDevelopersMailingList.

isJoinUsersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration

isJoinUsersMailingList.

isJSONValid(InputStream, InputStream) - Method in class net.sourceforge.seqware.common.util.jsontools.JSONHelper

Validates a json file against a schema to see if the file is valid

isLaunch() - Method in class net.sourceforge.seqware.common.model.Workflow

isLaunch.

isLIMSAdmin() - Method in class net.sourceforge.seqware.common.model.Registration

isLIMSAdmin.

isLocal() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

isLocal() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

Whether this job should run locally instead of out on a cluster.

isLocal() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

isLocked() - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock

Deprecated.

isLocked.

isMasterTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.BundleDir_Check

isMasterTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.CLICheck

isMasterTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_Check

isMasterTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_WS_ConsistencyCheck

isMasterTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.HDFS_Check

isMasterTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.Oozie_Check

isMasterTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.Script_Check

isMasterTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.TutorialCheck

isMasterTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.WS_Check

isMasterTest() - Method in interface io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface

isMetadataWriteBack() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

need metadata writeback? user can override this setting by using --no-metadata or --metadata from command line

isOozie(String) - Static method in class io.seqware.Engines

isOutput() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

is an output file?

isPairedEnd() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Get the value of pairedEnd

isPayee() - Method in class net.sourceforge.seqware.common.model.Registration

isPayee.

isPrivate() - Method in class net.sourceforge.seqware.common.model.Workflow

isPrivate.

isPublic() - Method in class net.sourceforge.seqware.common.model.Workflow

isPublic.

isReportInputFiles() - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

isRequireFiles() - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

isRequireFiles.

isSafe(String) - Static method in class net.sourceforge.seqware.common.util.Str

Whether or not the given string matches [a-zA-Z0-9_-]+

isSkipIfMissing() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

isSortable() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel

isStart() - Method in class net.sourceforge.solexatools.util.PageInfo

isStart.

isSubset(Set<T>, Set<T>) - Static method in class net.sourceforge.seqware.pipeline.tools.SetOperations

isSuperset(Set<T>, Set<T>) - Static method in class net.sourceforge.seqware.pipeline.tools.SetOperations

isTaskGroup() - Method in class net.sourceforge.seqware.common.model.Processing

isTaskGroup.

isTechnician() - Method in class net.sourceforge.seqware.common.model.Registration

isTechnician.

isToRunContained(Set<Integer>, Collection<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

Returns true if the filesToRun are totally contained by the files associated with the files in a given workflowRunAcc

isTutorialTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.BundleDir_Check

isTutorialTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.CLICheck

isTutorialTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_Check

isTutorialTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_WS_ConsistencyCheck

isTutorialTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.HDFS_Check

isTutorialTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.Oozie_Check

isTutorialTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.Script_Check

isTutorialTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.TutorialCheck

isTutorialTest() - Method in class io.seqware.pipeline.plugins.sanity.checks.WS_Check

isTutorialTest() - Method in interface io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface

isUseCheckFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

isUsePairedFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence

isUsePairedFile.

isVerbose() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

isVerbose.

isWait() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

wait for the workflow to finished, user can override this by using --wait from command line

isWorkflowRunAncesstor() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

isWorkflowRunAncesstor() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

ITUtility - Class in net.sourceforge.seqware.pipeline.plugins

ITUtility() - Constructor for class net.sourceforge.seqware.pipeline.plugins.ITUtility

Ius - Class in io.seqware.webservice.generated.model

Ius() - Constructor for class io.seqware.webservice.generated.model.Ius

Ius(Integer) - Constructor for class io.seqware.webservice.generated.model.Ius

Ius(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.Ius

IUS - Class in net.sourceforge.seqware.common.model

IUS() - Constructor for class net.sourceforge.seqware.common.model.IUS

Constructor for IUS.

IUS_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant IUS_ATTRIBUTES="Header.IUS_ATTRIBUTES.getTitle()"

IUS_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant

Constant IUS_PREFIX="ius_"

IUS_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant IUS_SWA="Header.IUS_SWA.getTitle()"

IUS_TAG - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant IUS_TAG="Header.IUS_TAG.getTitle()"

IUS_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant IUS_TAG_PREFIX="Header.IUS_TAG_PREFIX.getTitle()"

IusAttribute - Class in io.seqware.webservice.generated.model

IusAttribute() - Constructor for class io.seqware.webservice.generated.model.IusAttribute

IusAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.IusAttribute

IUSAttribute - Class in net.sourceforge.seqware.common.model

IusAttribute generated by hbm2java

IUSAttribute() - Constructor for class net.sourceforge.seqware.common.model.IUSAttribute

Constructor for IUSAttribute.

IUSAttribute(int, IUS) - Constructor for class net.sourceforge.seqware.common.model.IUSAttribute

Constructor for IUSAttribute.

IUSAttribute(int, IUS, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.IUSAttribute

Constructor for IUSAttribute.

IUSAttributeDAO - Interface in net.sourceforge.seqware.common.dao

IUSAttributeDAO interface.

IUSAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

IUSAttributeDAOHibernate class.

IUSAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate

IusAttributeFacadeREST - Class in io.seqware.webservice.generated.controller

IusAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.IusAttributeFacadeREST

IUSController - Class in net.sourceforge.solexatools.webapp.controller

IUSController class.

IUSController() - Constructor for class net.sourceforge.solexatools.webapp.controller.IUSController

Constructor for IUSController.

IUSController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.IUSController

Constructor for IUSController.

IUSDAO - Interface in net.sourceforge.seqware.common.dao

IUSDAO interface.

IUSDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

IUSDAOHibernate class.

IUSDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

Constructor for IUSDAOHibernate.

IusDto - Class in net.sourceforge.seqware.webservice.dto

IusDto() - Constructor for class net.sourceforge.seqware.webservice.dto.IusDto

IusFacadeREST - Class in io.seqware.webservice.generated.controller

IusFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.IusFacadeREST

IusFilesResource - Interface in net.sourceforge.seqware.webservice.resources.tables

IusFilesResource interface.

IusFilesServerResource - Class in net.sourceforge.seqware.webservice.resources.tables

IusFilesServerResource class.

IusFilesServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusFilesServerResource

Constructor for IusFilesServerResource.

IUSIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters

IUSIDFilter class.

IUSIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.IUSIDFilter

IusIDResource - Class in net.sourceforge.seqware.webservice.resources.tables

IusIDResource class.

IusIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusIDResource

Constructor for IusIDResource.

IusLink - Class in io.seqware.webservice.generated.model

IusLink() - Constructor for class io.seqware.webservice.generated.model.IusLink

IusLink(Integer) - Constructor for class io.seqware.webservice.generated.model.IusLink

IusLink(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.IusLink

IUSLink - Class in net.sourceforge.seqware.common.model

IusLink generated by hbm2java

IUSLink() - Constructor for class net.sourceforge.seqware.common.model.IUSLink

Constructor for IUSLink.

IUSLink(int, IUS, String, String) - Constructor for class net.sourceforge.seqware.common.model.IUSLink

Constructor for IUSLink.

IUSLink(int, IUS, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.IUSLink

Constructor for IUSLink.

IUSLinkDAO - Interface in net.sourceforge.seqware.common.dao.hibernate

IUSLinkDAO interface.

IUSLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

IUSLinkDAOHibernate class.

IUSLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate

IusLinkFacadeREST - Class in io.seqware.webservice.generated.controller

IusLinkFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.IusLinkFacadeREST

IUSList - Class in net.sourceforge.seqware.common.model.lists

IUSList class.

IUSList() - Constructor for class net.sourceforge.seqware.common.model.lists.IUSList

Constructor for IUSList.

IusResource - Class in net.sourceforge.seqware.webservice.resources.tables

IusResource class.

IusResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusResource

Constructor for IusResource.

IusSearchResource - Interface in net.sourceforge.seqware.webservice.resources.tables

IusSearchResource interface.

IusSearchServerResource - Class in net.sourceforge.seqware.webservice.resources.tables

IusSearchServerResource class.

IusSearchServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusSearchServerResource

Constructor for IusSearchServerResource.

IUSService - Interface in net.sourceforge.seqware.common.business

IUSService interface.

IUSServiceImpl - Class in net.sourceforge.seqware.common.business.impl

IUSServiceImpl class.

IUSServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

Constructor for IUSServiceImpl.

IUSSetupController - Class in net.sourceforge.solexatools.webapp.controller

IUSSetupController class.

IUSSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.IUSSetupController

IusWorkflowRuns - Class in io.seqware.webservice.generated.model

IusWorkflowRuns() - Constructor for class io.seqware.webservice.generated.model.IusWorkflowRuns

IusWorkflowRuns(Integer) - Constructor for class io.seqware.webservice.generated.model.IusWorkflowRuns

IusWorkflowRunsFacadeREST - Class in io.seqware.webservice.generated.controller

IusWorkflowRunsFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.IusWorkflowRunsFacadeREST

J

JavaJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model

JavaJob(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JavaJob

JavaSeqwareModuleJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model

JavaSeqwareModuleJob(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JavaSeqwareModuleJob

JaxbObject<T> - Class in net.sourceforge.seqware.common.util.xmltools

Convenience class for converting objects into JAXB XML.

JaxbObject() - Constructor for class net.sourceforge.seqware.common.util.xmltools.JaxbObject

JAXB has a memory leak when it comes to making new JAXBContext instances, so one JAXBContext is created for the entire lifetime of the program and initialized with all of the classes that we marshal and unmarshal at the moment, as per the instructions at * http://whileonefork.blogspot.com/2010/09/leaking-of-jaxb.html and * http://jaxb.java.net/guide/Performance_and_thread_safety.html .

JndiDatasourceCreator - Class in net.sourceforge.seqware.common.util.testtools

JndiDatasourceCreator class.

JndiDatasourceCreator() - Constructor for class net.sourceforge.seqware.common.util.testtools.JndiDatasourceCreator

Job - Interface in net.sourceforge.seqware.pipeline.workflowV2.model

JobBatch - Class in net.sourceforge.seqware.pipeline.workflowV2.model

JobBatch(String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

JobModule - Class in net.sourceforge.seqware.pipeline.workflowV2.model

JobModule class.

JobModule(Module) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule

Constructor for JobModule.

jobObj - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

jobObj - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

JobProfile - Class in net.sourceforge.seqware.pipeline.workflowV2.model

JobProfile class.

JobProfile(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile

Constructor for JobProfile.

JSON - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController

Constant JSON="json"

JSON - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant JSON="json"

JSONHelper - Class in net.sourceforge.seqware.common.util.jsontools

JSON Helper Class Contains methods related to parsing/validating of JSON which one may find useful

JSONHelper() - Constructor for class net.sourceforge.seqware.common.util.jsontools.JSONHelper

JsonUtil - Class in net.sourceforge.seqware.common.util.jsontools

JsonUtil class.

JsonUtil() - Constructor for class net.sourceforge.seqware.common.util.jsontools.JsonUtil

L

Lane - Class in io.seqware.webservice.generated.model

Lane() - Constructor for class io.seqware.webservice.generated.model.Lane

Lane(Integer) - Constructor for class io.seqware.webservice.generated.model.Lane

Lane(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.Lane

Lane - Class in net.sourceforge.seqware.common.model

Lane() - Constructor for class net.sourceforge.seqware.common.model.Lane

Constructor for Lane.

LANE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant LANE_ATTRIBUTES="Header.LANE_ATTRIBUTES.getTitle()"

LANE_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant LANE_NAME="Header.LANE_NAME.getTitle()"

LANE_NUM - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant LANE_NUM="Header.LANE_NUM.getTitle()"

LANE_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant

Constant LANE_PREFIX="seq_"

LANE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant LANE_SWA="Header.LANE_SWA.getTitle()"

LANE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant LANE_TAG_PREFIX="Header.LANE_TAG_PREFIX.getTitle()"

LaneAttribute - Class in io.seqware.webservice.generated.model

LaneAttribute() - Constructor for class io.seqware.webservice.generated.model.LaneAttribute

LaneAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.LaneAttribute

LaneAttribute - Class in net.sourceforge.seqware.common.model

LaneAttribute generated by hbm2java

LaneAttribute() - Constructor for class net.sourceforge.seqware.common.model.LaneAttribute

Constructor for LaneAttribute.

LaneAttribute(int, Lane) - Constructor for class net.sourceforge.seqware.common.model.LaneAttribute

Constructor for LaneAttribute.

LaneAttribute(int, Lane, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.LaneAttribute

Constructor for LaneAttribute.

LaneAttributeDAO - Interface in net.sourceforge.seqware.common.dao.hibernate

LaneAttributeDAO interface.

LaneAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

LaneAttributeDAOHibernate class.

LaneAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate

LaneAttributeFacadeREST - Class in io.seqware.webservice.generated.controller

LaneAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.LaneAttributeFacadeREST

LaneController - Class in net.sourceforge.solexatools.webapp.controller

LaneController

LaneController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneController

Constructor for LaneController.

LaneController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneController

Constructor for LaneController.

LaneDAO - Interface in net.sourceforge.seqware.common.dao

LaneDAO interface.

LaneDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

LaneDAOHibernate class.

LaneDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

Constructor for LaneDAOHibernate.

LaneFacadeREST - Class in io.seqware.webservice.generated.controller

LaneFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.LaneFacadeREST

LaneIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters

LaneIDFilter class.

LaneIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.LaneIDFilter

LaneIDResource - Class in net.sourceforge.seqware.webservice.resources.tables

LaneIDResource class.

LaneIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LaneIDResource

Constructor for LaneIDResource.

LaneInfo - Class in net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection

LaneInfo() - Constructor for class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

LaneLink - Class in io.seqware.webservice.generated.model

LaneLink() - Constructor for class io.seqware.webservice.generated.model.LaneLink

LaneLink(Integer) - Constructor for class io.seqware.webservice.generated.model.LaneLink

LaneLink(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.LaneLink

LaneLink - Class in net.sourceforge.seqware.common.model

LaneLink generated by hbm2java

LaneLink() - Constructor for class net.sourceforge.seqware.common.model.LaneLink

Constructor for LaneLink.

LaneLink(int, Lane, String, String) - Constructor for class net.sourceforge.seqware.common.model.LaneLink

Constructor for LaneLink.

LaneLink(int, Lane, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.LaneLink

Constructor for LaneLink.

LaneLinkDAO - Interface in net.sourceforge.seqware.common.dao.hibernate

LaneLinkDAO interface.

LaneLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

LaneLinkDAOHibernate class.

LaneLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate

LaneLinkFacadeREST - Class in io.seqware.webservice.generated.controller

LaneLinkFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.LaneLinkFacadeREST

LaneList - Class in net.sourceforge.seqware.common.model.lists

LaneList class.

LaneList() - Constructor for class net.sourceforge.seqware.common.model.lists.LaneList

Constructor for LaneList.

LaneResource - Class in net.sourceforge.seqware.webservice.resources.tables

LaneResource class.

LaneResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LaneResource

Constructor for LaneResource.

LaneSampleAssociateController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp

LaneSampleAssociateController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController

Constructor for LaneSampleAssociateController.

LaneSampleAssociateSetupController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp

LaneSampleAssociateSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController

Constructor for LaneSampleAssociateSetupController.

LaneService - Interface in net.sourceforge.seqware.common.business

LaneService interface.

LaneServiceImpl - Class in net.sourceforge.seqware.common.business.impl

LaneServiceImpl class.

LaneServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

Constructor for LaneServiceImpl.

LaneSetupController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController

LaneSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneSetupController

Constructor for LaneSetupController.

LaneType - Class in io.seqware.webservice.generated.model

LaneType() - Constructor for class io.seqware.webservice.generated.model.LaneType

LaneType(Integer) - Constructor for class io.seqware.webservice.generated.model.LaneType

LaneTypeFacadeREST - Class in io.seqware.webservice.generated.controller

LaneTypeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.LaneTypeFacadeREST

LaneValidator - Class in net.sourceforge.solexatools.validation

LaneValidator class.

LaneValidator() - Constructor for class net.sourceforge.solexatools.validation.LaneValidator

Constructor for LaneValidator.

LaneWorkflowRuns - Class in io.seqware.webservice.generated.model

LaneWorkflowRuns() - Constructor for class io.seqware.webservice.generated.model.LaneWorkflowRuns

LaneWorkflowRuns(Integer) - Constructor for class io.seqware.webservice.generated.model.LaneWorkflowRuns

LaneWorkflowRunsFacadeREST - Class in io.seqware.webservice.generated.controller

LaneWorkflowRunsFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.LaneWorkflowRunsFacadeREST

LAUNCH_SCHEDULED - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

launchBundle(String, String, String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>, Set<Integer>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

launchBundle.

launchBundle(String, String, String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>, Set<Integer>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine

launchBundle.

launchInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>, Set<Integer>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

launchInstalledBundle.

launchInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>, Set<Integer>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine

launchInstalledBundle.

launchNewWorkflow(OptionSet, Map<String, String>, String[], Metadata, Integer, Integer, String) - Static method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

Separating out the launching of a new workflow.

launchScheduledBundle(String, String, boolean, boolean) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

launchScheduledBundle.

launchScheduledBundle(String, String, boolean, boolean) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine

launchScheduledBundle.

launchSingleWorkflow(boolean) - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

Processes a single workflow

LaunchWorkflowController - Class in net.sourceforge.solexatools.webapp.controller

LaunchWorkflowController class.

LaunchWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController

Constructor for LaunchWorkflowController.

LaunchWorkflowListController - Class in net.sourceforge.solexatools.webapp.controller

LaunchWorkflowListController class.

LaunchWorkflowListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController

Constructor for LaunchWorkflowListController.

LaunchWorkflowListDetailsController - Class in net.sourceforge.solexatools.webapp.controller

LaunchWorkflowListDetailsController class.

LaunchWorkflowListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Constructor for LaunchWorkflowListDetailsController.

LaunchWorkflowSetupController - Class in net.sourceforge.solexatools.webapp.controller

LaunchWorkflowSetupController class.

LaunchWorkflowSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController

Constructor for LaunchWorkflowSetupController.

LaunchWorkflowUtil - Class in net.sourceforge.solexatools.util

LaunchWorkflowUtil class.

LaunchWorkflowUtil() - Constructor for class net.sourceforge.solexatools.util.LaunchWorkflowUtil

LEGACY_VAR_BUNDLE_DIR - Static variable in class net.sourceforge.seqware.common.util.maptools.MapTools

LEGACY_VAR_DATE - Static variable in class net.sourceforge.seqware.common.util.maptools.MapTools

LEGACY_VAR_RANDOM - Static variable in class net.sourceforge.seqware.common.util.maptools.MapTools

LibrariesResource - Class in net.sourceforge.seqware.webservice.resources.tables

LibrariesResource class.

LibrariesResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibrariesResource

Constructor for LibrariesResource.

LibraryDAO - Interface in net.sourceforge.seqware.common.dao

LibraryDAO interface.

LibraryDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

LibraryDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate

LibraryDto - Class in net.sourceforge.seqware.webservice.dto

LibraryDto() - Constructor for class net.sourceforge.seqware.webservice.dto.LibraryDto

LibraryIdentityDto - Class in net.sourceforge.seqware.webservice.dto

LibraryIdentityDto() - Constructor for class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto

LibraryResource - Class in net.sourceforge.seqware.webservice.resources.tables

LibraryResource class.

LibraryResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibraryResource

Constructor for LibraryResource.

LibrarySelection - Class in io.seqware.webservice.generated.model

LibrarySelection() - Constructor for class io.seqware.webservice.generated.model.LibrarySelection

LibrarySelection(Integer) - Constructor for class io.seqware.webservice.generated.model.LibrarySelection

LibrarySelection - Class in net.sourceforge.seqware.common.model

LibrarySelection class.

LibrarySelection() - Constructor for class net.sourceforge.seqware.common.model.LibrarySelection

Constructor for LibrarySelection.

LibrarySelectionDAO - Interface in net.sourceforge.seqware.common.dao

LibrarySelectionDAO interface.

LibrarySelectionDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

LibrarySelectionDAOHibernate class.

LibrarySelectionDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate

Constructor for LibrarySelectionDAOHibernate.

LibrarySelectionFacadeREST - Class in io.seqware.webservice.generated.controller

LibrarySelectionFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.LibrarySelectionFacadeREST

LibrarySelectionList - Class in net.sourceforge.seqware.common.model.lists

LibrarySelectionList class.

LibrarySelectionList() - Constructor for class net.sourceforge.seqware.common.model.lists.LibrarySelectionList

Constructor for LibrarySelectionList.

LibrarySelectionResource - Class in net.sourceforge.seqware.webservice.resources.tables

ExperimentResource class.

LibrarySelectionResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibrarySelectionResource

Constructor for ExperimentResource.

LibrarySelectionService - Interface in net.sourceforge.seqware.common.business

LibrarySelectionService interface.

LibrarySelectionServiceImpl - Class in net.sourceforge.seqware.common.business.impl

LibrarySelectionServiceImpl class.

LibrarySelectionServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl

Constructor for LibrarySelectionServiceImpl.

LibraryService - Interface in net.sourceforge.seqware.common.business

LibraryService interface.

LibraryServiceImpl - Class in net.sourceforge.seqware.common.business.impl

LibraryServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl

LibrarySource - Class in io.seqware.webservice.generated.model

LibrarySource() - Constructor for class io.seqware.webservice.generated.model.LibrarySource

LibrarySource(Integer) - Constructor for class io.seqware.webservice.generated.model.LibrarySource

LibrarySource - Class in net.sourceforge.seqware.common.model

LibrarySource class.

LibrarySource() - Constructor for class net.sourceforge.seqware.common.model.LibrarySource

Constructor for LibrarySource.

LibrarySourceDAO - Interface in net.sourceforge.seqware.common.dao

LibrarySourceDAO interface.

LibrarySourceDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

LibrarySourceDAOHibernate class.

LibrarySourceDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate

Constructor for LibrarySourceDAOHibernate.

LibrarySourceFacadeREST - Class in io.seqware.webservice.generated.controller

LibrarySourceFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.LibrarySourceFacadeREST

LibrarySourceList - Class in net.sourceforge.seqware.common.model.lists

LibrarySourceList class.

LibrarySourceList() - Constructor for class net.sourceforge.seqware.common.model.lists.LibrarySourceList

Constructor for LibrarySourceList.

LibrarySourceResource - Class in net.sourceforge.seqware.webservice.resources.tables

ExperimentResource class.

LibrarySourceResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibrarySourceResource

Constructor for ExperimentResource.

LibrarySourceService - Interface in net.sourceforge.seqware.common.business

LibrarySourceService interface.

LibrarySourceServiceImpl - Class in net.sourceforge.seqware.common.business.impl

LibrarySourceServiceImpl class.

LibrarySourceServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl

Constructor for LibrarySourceServiceImpl.

LibraryStrategy - Class in io.seqware.webservice.generated.model

LibraryStrategy() - Constructor for class io.seqware.webservice.generated.model.LibraryStrategy

LibraryStrategy(Integer) - Constructor for class io.seqware.webservice.generated.model.LibraryStrategy

LibraryStrategy - Class in net.sourceforge.seqware.common.model

LibraryStrategy class.

LibraryStrategy() - Constructor for class net.sourceforge.seqware.common.model.LibraryStrategy

Constructor for LibraryStrategy.

LibraryStrategyDAO - Interface in net.sourceforge.seqware.common.dao

LibraryStrategyDAO interface.

LibraryStrategyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

LibraryStrategyDAOHibernate class.

LibraryStrategyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate

Constructor for LibraryStrategyDAOHibernate.

LibraryStrategyFacadeREST - Class in io.seqware.webservice.generated.controller

LibraryStrategyFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.LibraryStrategyFacadeREST

LibraryStrategyList - Class in net.sourceforge.seqware.common.model.lists

LibraryStrategyList class.

LibraryStrategyList() - Constructor for class net.sourceforge.seqware.common.model.lists.LibraryStrategyList

Constructor for LibraryStrategyList.

LibraryStrategyResource - Class in net.sourceforge.seqware.webservice.resources.tables

ExperimentResource class.

LibraryStrategyResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibraryStrategyResource

Constructor for ExperimentResource.

LibraryStrategyService - Interface in net.sourceforge.seqware.common.business

LibraryStrategyService interface.

LibraryStrategyServiceImpl - Class in net.sourceforge.seqware.common.business.impl

LibraryStrategyServiceImpl class.

LibraryStrategyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl

Constructor for LibraryStrategyServiceImpl.

linkAccessionAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

linkAccessionAndParent.

linkAccessionAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

linkAccessionAndParent.

linkProcessingAndFile(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

linkProcessingAndFile.

linkWorkflowRunAndParent(int, int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

linkWorkflowRunAndParent.

linkWorkflowRunAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

linkWorkflowRunAndParent.

linkWorkflowRunAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

linkWorkflowRunAndParent.

linkWorkflowRunAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

linkWorkflowRunAndParent.

linkWorkflowRunAndParent(WorkflowRun, int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager

linkWorkflowRunAndParent.

list() - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ExperimentService

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

list.

list(Study) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService

list.

list() - Method in interface net.sourceforge.seqware.common.business.FileService

list.

list() - Method in interface net.sourceforge.seqware.common.business.FileTypeService

list.

list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl

list.

list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

list.

list(Study) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl

list.

list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl

list.

list(Registration, InvoiceState) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

list.

list(List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

list.

list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl

list.

list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl

list.

list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl

list.

list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl

list.

list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

list.

list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

list.

list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl

list.

list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

list.

list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

list.

list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

list.

list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

list.

list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

list.

list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

list.

list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

list.

list() - Method in interface net.sourceforge.seqware.common.business.InvoiceService

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.business.InvoiceService

list.

list(Registration, InvoiceState) - Method in interface net.sourceforge.seqware.common.business.InvoiceService

list.

list() - Method in interface net.sourceforge.seqware.common.business.IUSService

list.

list(List<Integer>) - Method in interface net.sourceforge.seqware.common.business.LaneService

list.

list() - Method in interface net.sourceforge.seqware.common.business.LaneService

list.

list() - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService

list.

list() - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService

list.

list() - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService

list.

list() - Method in interface net.sourceforge.seqware.common.business.OrganismService

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.business.OrganismService

list.

list() - Method in interface net.sourceforge.seqware.common.business.PlatformService

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.business.PlatformService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ProcessingService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService

list.

list() - Method in interface net.sourceforge.seqware.common.business.SampleSearchService

list.

list() - Method in interface net.sourceforge.seqware.common.business.SampleService

list.

list() - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

list.

list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ShareFileService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ShareLaneService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ShareSampleService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ShareStudyService

list.

list() - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.business.StudyService

list.

list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService

list.

list() - Method in interface net.sourceforge.seqware.common.business.StudyService

list.

list() - Method in interface net.sourceforge.seqware.common.business.StudyTypeService

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService

list.

list() - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService

list.

list() - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService

list.

list() - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService

list.

list() - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

list.

list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

list.

list() - Method in interface net.sourceforge.seqware.common.business.WorkflowService

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

list.

list(Study) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.FileDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.FileTypeDAO

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate

list.

list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

list.

list(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

list.

list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate

list.

list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate

list.

list(Registration, InvoiceState) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

list.

list(List<Integer>) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

list.

list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate

list.

list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate

list.

list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate

list.

list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate

list.

list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate

list.

list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate

list.

list(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate

list.

list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate

list.

list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

list.

list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

list.

list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

list.

list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate

list.

list() - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO

list.

list(Registration, InvoiceState) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

list.

list(List<Integer>) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.SampleSearchDAO

list.

list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO

list.

list(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO

list.

list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

list.

list(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

list.

list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

list.

list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO

list.

listByParentProcessingId(int) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl

listByParentProcessingId(int) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService

listByParentProcessingId(int) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate

listByParentProcessingId(int) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO

listComplete() - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

listComplete.

listComplete() - Method in interface net.sourceforge.seqware.common.business.SampleService

listComplete.

listComplete() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

listComplete.

listComplete() - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

listComplete.

listFields(String) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

list the fields available to set

listFile(Registration, String, List<File>, String[], String[]) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

listFile.

listFile(Registration, String, List<File>, String[], String[]) - Method in interface net.sourceforge.seqware.common.business.LaneService

listFile.

listFilesRecursive(File, ArrayList<File>) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

listFilesRecursive.

listIncomplete() - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

listIncomplete.

listIncomplete() - Method in interface net.sourceforge.seqware.common.business.SampleService

listIncomplete.

listIncomplete() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

listIncomplete.

listIncomplete() - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

listIncomplete.

listInstalledWorkflowParams(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

listInstalledWorkflowParams.

listInstalledWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

listInstalledWorkflowParams.

listInstalledWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

listInstalledWorkflowParams.

listInstalledWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

listInstalledWorkflowParams.

listInstalledWorkflows() - Method in interface net.sourceforge.seqware.common.metadata.Metadata

listInstalledWorkflows.

listInstalledWorkflows() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

listInstalledWorkflows.

listInstalledWorkflows() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

listInstalledWorkflows.

listInstalledWorkflows() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

listInstalledWorkflows.

listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

listMyShared.

listMyShared(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

listMyShared.

listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

listMyShared.

listMyShared(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

listMyShared.

listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService

listMyShared.

listMyShared(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

listMyShared.

listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

listMyShared.

listMyShared(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

listMyShared.

listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

listMyShared.

listMyShared(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

listMyShared.

listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

listMyShared.

listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

listMyShared.

listMyShared(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

listMyShared.

listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

listMyShared.

listRelatedWorkflows(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

listRelatedWorkflows.

listRelatedWorkflows(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

listRelatedWorkflows.

listRelatedWorkflows(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

listRelatedWorkflows.

listRelatedWorkflows(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

listRelatedWorkflows.

listRunning(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

listRunning.

listRunning(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

listRunning.

listRunning(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

listRunning.

listRunning(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

listRunning.

listRunning(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

listRunning.

listRunning(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

listRunning.

listSample(Registration) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

listSample.

listSample(Registration) - Method in interface net.sourceforge.seqware.common.business.SampleService

listSample.

listSample(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

listSample.

listSample(Registration) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

listSample.

listSequencerRunsWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

listSequencerRunsWorkflows.

listSequencerRunsWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

listSequencerRunsWorkflows.

listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

listSharedWithMe.

listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

listSharedWithMe.

listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

listSharedWithMe.

listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

listSharedWithMe.

listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

listSharedWithMe.

listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.business.StudyService

listSharedWithMe.

listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService

listSharedWithMe.

listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

listSharedWithMe.

listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

listSharedWithMe.

listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

listSharedWithMe.

listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

listSharedWithMe.

listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

listSharedWithMe.

listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

listSharedWithMe.

listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

listSharedWithMe.

listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

listSharedWithMe.

listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

listSharedWithMe.

listSharedWithMeWithSample(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

listSharedWithMeWithSample.

listSharedWithMeWithSample(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

listSharedWithMeWithSample.

listStudyHasFile(Registration, String, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

listStudyHasFile.

listStudyHasFile(Registration, String, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService

listStudyHasFile.

listStudyHasFile(Registration, String, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

listStudyHasFile.

listStudyHasFile(Registration, String, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

listStudyHasFile.

listWithHasFile(SortedSet<Experiment>, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

listWithHasFile.

listWithHasFile(SortedSet<Experiment>, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

listWithHasFile.

listWithHasFile(SortedSet<IUS>, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

listWithHasFile.

listWithHasFile(SortedSet<Lane>, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

listWithHasFile.

listWithHasFile(Integer, SortedSet<Sample>, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

listWithHasFile.

listWithHasFile(List<Study>) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

listWithHasFile.

listWithHasFile(List<Study>, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

listWithHasFile.

listWithHasFile(List<WorkflowRun>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

listWithHasFile.

listWithHasFile(SortedSet<IUS>, String) - Method in interface net.sourceforge.seqware.common.business.IUSService

listWithHasFile.

listWithHasFile(SortedSet<Lane>, String) - Method in interface net.sourceforge.seqware.common.business.LaneService

listWithHasFile.

listWithHasFile(Integer, SortedSet<Sample>, String) - Method in interface net.sourceforge.seqware.common.business.SampleService

listWithHasFile.

listWithHasFile(List<Study>) - Method in interface net.sourceforge.seqware.common.business.StudyService

listWithHasFile.

listWithHasFile(List<Study>, String) - Method in interface net.sourceforge.seqware.common.business.StudyService

listWithHasFile.

listWithHasFile(List<WorkflowRun>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

listWithHasFile.

listWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

listWorkflows.

listWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

listWorkflows.

LoadIndexPageController - Class in net.sourceforge.solexatools.webapp.controller

LoadIndexPageController class.

LoadIndexPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController

Constructor for LoadIndexPageController.

lockAndAppend(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.lock.LockingFileTools

lockAndAppendLine(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.lock.LockingFileTools

lockAndAppendLine.

lockAndWrite(File, String, boolean) - Static method in class net.sourceforge.seqware.common.util.filetools.lock.LockingFileTools

Try to acquire lock.

LockingFileTools - Class in net.sourceforge.seqware.common.util.filetools.lock

LockingFileTools class.

LockingFileTools() - Constructor for class net.sourceforge.seqware.common.util.filetools.lock.LockingFileTools

Log - Class in net.sourceforge.seqware.common.util

Log class.

LoginController - Class in net.sourceforge.solexatools.webapp.controller

LoginController

LoginController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LoginController

Constructor for LoginController.

loginSuccess(String, String) - Method in class net.sourceforge.solexatools.authentication.Authentication

loginSuccess.

loginSuccess(String, String) - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication

loginSuccess.

loginSuccess(String, String) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos

loginSuccess.

LoginValidator - Class in net.sourceforge.solexatools.validation

LoginValidator class.

LoginValidator() - Constructor for class net.sourceforge.solexatools.validation.LoginValidator

Constructor for LoginValidator.

LogoutController - Class in net.sourceforge.solexatools.webapp.controller

LogoutController class.

LogoutController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LogoutController

Constructor for LogoutController.

M

Main - Class in io.seqware.cli

Main() - Constructor for class io.seqware.cli.Main

main(String[]) - Static method in class io.seqware.cli.Main

main(String[]) - Static method in class io.seqware.pipeline.plugins.sanity.SanityCheck

main(String[]) - Static method in class io.seqware.webservice.client.SeqWareWebServiceClient

Example for using the client

main(String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools

main.

main(String[]) - Static method in class net.sourceforge.seqware.common.util.TabExpansionUtil

main(String[]) - Static method in class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator

main.

main(String[]) - Static method in class net.sourceforge.seqware.pipeline.module.TestModule

main.

main(String[]) - Static method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection

main(String[]) - Static method in class net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB

main(String[]) - Static method in class net.sourceforge.seqware.pipeline.plugins.deletion.DeletionDB

main(String[]) - Static method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin

main(String[]) - Static method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin

main(String[]) - Static method in class net.sourceforge.seqware.pipeline.runner.PluginRunner

main.

main(String[]) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner

main.

main(String[]) - Static method in class net.sourceforge.seqware.pipeline.tools.ReportTest

main.

main(String[]) - Static method in class net.sourceforge.seqware.pipeline.tools.UnZip

main.

main(String[]) - Static method in class net.sourceforge.seqware.pipeline.tools.Zip

main.

main(String[]) - Static method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceMain

main.

makeReport(String) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport

makeReport.

ManageWorkflowsController - Class in net.sourceforge.solexatools.webapp.controller

ManageWorkflowsController class.

ManageWorkflowsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController

Constructor for ManageWorkflowsController.

mappedParam - Variable in enum net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility.HumanProvenanceFilters

mapProcessingIdToAccession(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

mapProcessingIdToAccession.

mapProcessingIdToAccession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

mapProcessingIdToAccession.

mapProcessingIdToAccession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

mapProcessingIdToAccession.

mapProcessingIdToAccession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

mapProcessingIdToAccession.

mapString2Int(Map) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools

mapString2Int.

MapTools - Class in net.sourceforge.seqware.common.util.maptools

MapTools class.

MapTools() - Constructor for class net.sourceforge.seqware.common.util.maptools.MapTools

markDatabaseChanged() - Static method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreatorWrapper

markDatabaseChanged.

markDatabaseChanged() - Static method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

markDatabaseChanged.

MarkdownPlugin - Class in net.sourceforge.seqware.pipeline.plugins

This plugin outputs documentation for our plugins and modules in markdown format

MarkdownPlugin() - Constructor for class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin

Constructor for HelloWorld.

MarkdownPlugin.MarkDownFormatter - Class in net.sourceforge.seqware.pipeline.plugins

MarkdownPlugin.MarkDownFormatter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.MarkDownFormatter

MarkdownPlugin.ModuleComparator - Class in net.sourceforge.seqware.pipeline.plugins

MarkdownPlugin.ModuleComparator() - Constructor for class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.ModuleComparator

MarkdownPlugin.PluginComparator - Class in net.sourceforge.seqware.pipeline.plugins

MarkdownPlugin.PluginComparator() - Constructor for class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.PluginComparator

marshal(Date) - Method in class io.seqware.webservice.adapter.DateFormatterAdapter

marshal(Timestamp) - Method in class io.seqware.webservice.adapter.TimestampFormatterAdapter

marshal(Set<File>) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeFileSet

marshal(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeIUSSortedSet

marshal(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeLaneSortedSet

marshal(String) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeXML

marshal(T) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject

Turn an object into XML using JAXB and provide the result in a StreamResult.

marshalToDocument(T) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject

Turn an object into XML using JAXB and provide the result in a StreamResult.

marshalToDocument(JaxbObject, Object) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools

marshalToDocument.

matchName(String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

matchName(String) - Method in interface net.sourceforge.seqware.common.business.SampleService

matchName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

findByName.

matchName(String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

findByName.

MAX_FILE_NAME_SIZE - Static variable in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter

maxMemorySgeParamFormat - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

MD5Generator - Class in net.sourceforge.seqware.common.util

Utility class for calculating MD5 hash on a file's contents.

MD5Generator() - Constructor for class net.sourceforge.seqware.common.util.MD5Generator

md5sum(String) - Method in class net.sourceforge.seqware.common.util.MD5Generator

Returns a 32 character representation of the MD5 hash of the specified file's content.

md5sumFile(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

md5sumFile.

merge(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

merge.

merge(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

merge.

merge(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

merge.

merge(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService

merge.

merge(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

merge.

merge(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

merge.

merge(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

merge.

merge(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

merge.

merge(String, String, Map) - Static method in class net.sourceforge.seqware.common.util.freemarker.Freemarker

merge.

mergeAttributes(Set<T>, Set<T>, S) - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource

Merge attributes from a new set into an existing one while removing duplicates.

Metadata - Interface in net.sourceforge.seqware.common.metadata

metadata - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle

metadata - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin

Metadata - Class in net.sourceforge.seqware.pipeline.plugins

This plugin currently lets users creation a limited set of table rows in the database from the command line.

Metadata() - Constructor for class net.sourceforge.seqware.pipeline.plugins.Metadata

Constructor for Metadata.

metadata - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

MetadataDB - Class in net.sourceforge.seqware.common.metadata

MetadataDB class.

MetadataDB(Connection) - Constructor for class net.sourceforge.seqware.common.metadata.MetadataDB

MetadataDB(DataSource) - Constructor for class net.sourceforge.seqware.common.metadata.MetadataDB

MetadataDB(String, String, String) - Constructor for class net.sourceforge.seqware.common.metadata.MetadataDB

MetadataDB - Class in net.sourceforge.seqware.queryengine.webservice.model

MetadataDB class.

MetadataDB() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB

MetadataDB.IntByIndex - Class in net.sourceforge.seqware.common.metadata

MetadataDB.IntByIndex(int, int) - Constructor for class net.sourceforge.seqware.common.metadata.MetadataDB.IntByIndex

MetadataDB.IntByName - Class in net.sourceforge.seqware.common.metadata

MetadataDB.IntByName(String, int) - Constructor for class net.sourceforge.seqware.common.metadata.MetadataDB.IntByName

MetadataFactory - Class in net.sourceforge.seqware.common.metadata

MetadataFactory() - Constructor for class net.sourceforge.seqware.common.metadata.MetadataFactory

METADATAINVALIDIDCHAIN - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant METADATAINVALIDIDCHAIN=8

MetadataNoConnection - Class in net.sourceforge.seqware.common.metadata

MetadataNoConnection class.

MetadataNoConnection() - Constructor for class net.sourceforge.seqware.common.metadata.MetadataNoConnection

metadataWriteback - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

MetadataWS - Class in net.sourceforge.seqware.common.metadata

MetadataWS(String, String, String) - Constructor for class net.sourceforge.seqware.common.metadata.MetadataWS

Constructor for MetadataWS.

MetadataWS.LowLevel - Class in net.sourceforge.seqware.common.metadata

MetadataWS.LowLevel(String, String, String) - Constructor for class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel

metaMap - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

ModelAccessionIDTuple - Class in io.seqware.webservice.controller

Holds information for the recursive deletion tool

ModelAccessionIDTuple() - Constructor for class io.seqware.webservice.controller.ModelAccessionIDTuple

ModelAccessionIDTuple(int, int, String) - Constructor for class io.seqware.webservice.controller.ModelAccessionIDTuple

ModelAccessionIDTuple - Class in io.seqware.webservice.generated.controller

Holds information for the recursive deletion tool

ModelAccessionIDTuple() - Constructor for class io.seqware.webservice.generated.controller.ModelAccessionIDTuple

ModelAccessionIDTuple(int, int, String) - Constructor for class io.seqware.webservice.generated.controller.ModelAccessionIDTuple

ModelUtil - Class in net.sourceforge.solexatools.util

ModelUtil class.

ModelUtil() - Constructor for class net.sourceforge.solexatools.util.ModelUtil

modifyIniFile(String, String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

Module - Class in net.sourceforge.seqware.pipeline.module

Abstract Module class.

Module() - Constructor for class net.sourceforge.seqware.pipeline.module.Module

Module - Enum in net.sourceforge.seqware.pipeline.workflowV2.model

Module class.

ModuleInterface - Interface in net.sourceforge.seqware.pipeline.module

This interface defines the required behavior of a SeqWare module.

ModuleMethod - Enum in net.sourceforge.seqware.pipeline.module

Enumeration class for ModuleMethod Created by IntelliJ IDEA.

ModuleRunner - Class in net.sourceforge.seqware.pipeline.plugins

ModuleRunner class.

ModuleRunner() - Constructor for class net.sourceforge.seqware.pipeline.plugins.ModuleRunner

Constructor for ModuleRunner.

N

NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService

Constant NAME="ExperimentLibraryDesignService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentService

Constant NAME="ExperimentService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService

Constant NAME="ExperimentSpotDesignReadSpecService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService

Constant NAME="ExperimentSpotDesignService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.FileService

Constant NAME="fileService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.FileTypeService

Constant NAME="FileTypeService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.FileUploadService

Constant NAME="FileUploadService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.InvoiceService

Constant NAME="invoiceService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.IUSService

Constant NAME="IUSService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.LaneService

Constant NAME="laneService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.LibrarySelectionService

Constant NAME="LibrarySelectionService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.LibrarySourceService

Constant NAME="LibrarySourceService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.LibraryStrategyService

Constant NAME="LibraryStrategyService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.OrganismService

Constant NAME="OrganismService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.PlatformService

Constant NAME="PlatformService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.ProcessingService

Constant NAME="processingService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.RegistrationService

Constant NAME="registrationService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.SampleService

Constant NAME="sampleService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.SequencerRunService

Constant NAME="SequencerRunService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.ShareStudyService

Constant NAME="shareStudyService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService

Constant NAME="shareWorkflowRunService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.StudyService

Constant NAME="StudyService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.StudyTypeService

Constant NAME="StudyTypeService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowParamService

Constant NAME="workflowParamService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowParamValueService

Constant NAME="WorkflowParamValueService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowRunParamService

Constant NAME="WorkflowRunParamService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowRunService

Constant NAME="WorkflowRunService"

NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowService

Constant NAME="WorkflowService"

name - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

NAMESPACE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp

NAMESPACE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag

net.sourceforge.seqware.common - package net.sourceforge.seqware.common

net.sourceforge.seqware.common.business - package net.sourceforge.seqware.common.business

net.sourceforge.seqware.common.business.impl - package net.sourceforge.seqware.common.business.impl

net.sourceforge.seqware.common.dao - package net.sourceforge.seqware.common.dao

net.sourceforge.seqware.common.dao.hibernate - package net.sourceforge.seqware.common.dao.hibernate

net.sourceforge.seqware.common.err - package net.sourceforge.seqware.common.err

net.sourceforge.seqware.common.factory - package net.sourceforge.seqware.common.factory

net.sourceforge.seqware.common.hibernate - package net.sourceforge.seqware.common.hibernate

net.sourceforge.seqware.common.hibernate.reports - package net.sourceforge.seqware.common.hibernate.reports

net.sourceforge.seqware.common.invitation - package net.sourceforge.seqware.common.invitation

net.sourceforge.seqware.common.metadata - package net.sourceforge.seqware.common.metadata

net.sourceforge.seqware.common.model - package net.sourceforge.seqware.common.model

net.sourceforge.seqware.common.model.adapters - package net.sourceforge.seqware.common.model.adapters

net.sourceforge.seqware.common.model.comparator - package net.sourceforge.seqware.common.model.comparator

net.sourceforge.seqware.common.model.lists - package net.sourceforge.seqware.common.model.lists

net.sourceforge.seqware.common.module - package net.sourceforge.seqware.common.module

net.sourceforge.seqware.common.security - package net.sourceforge.seqware.common.security

net.sourceforge.seqware.common.util - package net.sourceforge.seqware.common.util

net.sourceforge.seqware.common.util.configtools - package net.sourceforge.seqware.common.util.configtools

net.sourceforge.seqware.common.util.exceptiontools - package net.sourceforge.seqware.common.util.exceptiontools

net.sourceforge.seqware.common.util.filetools - package net.sourceforge.seqware.common.util.filetools

net.sourceforge.seqware.common.util.filetools.lock - package net.sourceforge.seqware.common.util.filetools.lock

net.sourceforge.seqware.common.util.filetools.validate - package net.sourceforge.seqware.common.util.filetools.validate

net.sourceforge.seqware.common.util.freemarker - package net.sourceforge.seqware.common.util.freemarker

net.sourceforge.seqware.common.util.iotools - package net.sourceforge.seqware.common.util.iotools

net.sourceforge.seqware.common.util.jsontools - package net.sourceforge.seqware.common.util.jsontools

net.sourceforge.seqware.common.util.maptools - package net.sourceforge.seqware.common.util.maptools

net.sourceforge.seqware.common.util.processtools - package net.sourceforge.seqware.common.util.processtools

net.sourceforge.seqware.common.util.processtools.stderr - package net.sourceforge.seqware.common.util.processtools.stderr

net.sourceforge.seqware.common.util.processtools.stdout - package net.sourceforge.seqware.common.util.processtools.stdout

net.sourceforge.seqware.common.util.runtools - package net.sourceforge.seqware.common.util.runtools

net.sourceforge.seqware.common.util.testtools - package net.sourceforge.seqware.common.util.testtools

net.sourceforge.seqware.common.util.workflowtools - package net.sourceforge.seqware.common.util.workflowtools

net.sourceforge.seqware.common.util.xmltools - package net.sourceforge.seqware.common.util.xmltools

net.sourceforge.seqware.metadb.util - package net.sourceforge.seqware.metadb.util

net.sourceforge.seqware.pipeline.bundle - package net.sourceforge.seqware.pipeline.bundle

net.sourceforge.seqware.pipeline.daxgenerator - package net.sourceforge.seqware.pipeline.daxgenerator

net.sourceforge.seqware.pipeline.decider - package net.sourceforge.seqware.pipeline.decider

net.sourceforge.seqware.pipeline.deciders - package net.sourceforge.seqware.pipeline.deciders

net.sourceforge.seqware.pipeline.module - package net.sourceforge.seqware.pipeline.module

This package provides the SeqWare module interface and API, including common code and classes.

net.sourceforge.seqware.pipeline.module.ann - package net.sourceforge.seqware.pipeline.module.ann

net.sourceforge.seqware.pipeline.modules - package net.sourceforge.seqware.pipeline.modules

net.sourceforge.seqware.pipeline.modules.utilities - package net.sourceforge.seqware.pipeline.modules.utilities

net.sourceforge.seqware.pipeline.plugin - package net.sourceforge.seqware.pipeline.plugin

net.sourceforge.seqware.pipeline.plugins - package net.sourceforge.seqware.pipeline.plugins

net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection - package net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection

net.sourceforge.seqware.pipeline.plugins.checkdb - package net.sourceforge.seqware.pipeline.plugins.checkdb

net.sourceforge.seqware.pipeline.plugins.checkdb.plugins - package net.sourceforge.seqware.pipeline.plugins.checkdb.plugins

net.sourceforge.seqware.pipeline.plugins.deletion - package net.sourceforge.seqware.pipeline.plugins.deletion

net.sourceforge.seqware.pipeline.plugins.filelinker - package net.sourceforge.seqware.pipeline.plugins.filelinker

net.sourceforge.seqware.pipeline.plugins.fileprovenance - package net.sourceforge.seqware.pipeline.plugins.fileprovenance

net.sourceforge.seqware.pipeline.runner - package net.sourceforge.seqware.pipeline.runner

net.sourceforge.seqware.pipeline.tools - package net.sourceforge.seqware.pipeline.tools

net.sourceforge.seqware.pipeline.workflow - package net.sourceforge.seqware.pipeline.workflow

net.sourceforge.seqware.pipeline.workflowV2 - package net.sourceforge.seqware.pipeline.workflowV2

net.sourceforge.seqware.pipeline.workflowV2.engine.oozie - package net.sourceforge.seqware.pipeline.workflowV2.engine.oozie

net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object - package net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object

net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus - package net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus

net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object - package net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object

net.sourceforge.seqware.pipeline.workflowV2.model - package net.sourceforge.seqware.pipeline.workflowV2.model

net.sourceforge.seqware.queryengine.webservice.controller - package net.sourceforge.seqware.queryengine.webservice.controller

net.sourceforge.seqware.queryengine.webservice.model - package net.sourceforge.seqware.queryengine.webservice.model

net.sourceforge.seqware.queryengine.webservice.security - package net.sourceforge.seqware.queryengine.webservice.security

net.sourceforge.seqware.queryengine.webservice.util - package net.sourceforge.seqware.queryengine.webservice.util

net.sourceforge.seqware.queryengine.webservice.view - package net.sourceforge.seqware.queryengine.webservice.view

net.sourceforge.seqware.webservice.dto - package net.sourceforge.seqware.webservice.dto

net.sourceforge.seqware.webservice.resources - package net.sourceforge.seqware.webservice.resources

net.sourceforge.seqware.webservice.resources.filters - package net.sourceforge.seqware.webservice.resources.filters

net.sourceforge.seqware.webservice.resources.queries - package net.sourceforge.seqware.webservice.resources.queries

net.sourceforge.seqware.webservice.resources.tables - package net.sourceforge.seqware.webservice.resources.tables

net.sourceforge.solexatools - package net.sourceforge.solexatools

net.sourceforge.solexatools.authentication - package net.sourceforge.solexatools.authentication

net.sourceforge.solexatools.util - package net.sourceforge.solexatools.util

net.sourceforge.solexatools.validation - package net.sourceforge.solexatools.validation

net.sourceforge.solexatools.webapp.controller - package net.sourceforge.solexatools.webapp.controller

net.sourceforge.solexatools.webapp.metamodel - package net.sourceforge.solexatools.webapp.metamodel

NewSeqwareStyle - Annotation Type in net.sourceforge.seqware.pipeline.module.ann

This Annotation is used to tag a ModuleInterface.

nextInvitationCode() - Method in class net.sourceforge.seqware.common.invitation.RandomInvitationCode

nextInvitationCode.

nextInvitationCode() - Method in class net.sourceforge.solexatools.util.RandomInvitationCode

nextInvitationCode.

NO_DATABASE_CONFIG - Static variable in class net.sourceforge.seqware.common.metadata.MetadataFactory

NodeHtmlUtil - Class in net.sourceforge.solexatools.util

NodeHtmlUtil class.

NodeHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.NodeHtmlUtil

NoExitSecurityManager - Class in net.sourceforge.seqware.common.util

Created by IntelliJ IDEA.

NoExitSecurityManager() - Constructor for class net.sourceforge.seqware.common.util.NoExitSecurityManager

NotFoundException - Exception in net.sourceforge.seqware.common.err

NotFoundException class.

NotFoundException() - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException

Constructor for NotFoundException.

NotFoundException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException

Constructor for NotFoundException.

NotFoundException(String) - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException

Constructor for NotFoundException.

NotFoundException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException

Constructor for NotFoundException.

NOTIMPLEMENTED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant NOTIMPLEMENTED=-1

NS - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

NULL - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant NULL=-99

NullBeanUtils - Class in net.sourceforge.seqware.common.util

NullBeanUtils class.

NullBeanUtils() - Constructor for class net.sourceforge.seqware.common.util.NullBeanUtils

NUMBER_TO_OUTPUT - Static variable in class io.seqware.pipeline.plugins.sanity.SanityCheck

NUMBER_TO_OUTPUT - Static variable in class net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB

O

OICRLdapAuthentication - Class in net.sourceforge.solexatools.authentication

This authentication plugin allows the SeqWare Portal to authenticate against the Ontario Institute for Cancer Research (OICR) LDAP server.

OICRLdapAuthentication() - Constructor for class net.sourceforge.solexatools.authentication.OICRLdapAuthentication

okTo - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

OldSeqwareException - Exception in net.sourceforge.seqware.common.err

This exception wraps the old seqware exception code User: Xiaoshu Wang (xiao@renci.org) Date: 9/6/11 Time: 2:38 PM

OldSeqwareException() - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException

Constructor for OldSeqwareException.

OldSeqwareException(String) - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException

Constructor for OldSeqwareException.

OldSeqwareException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException

Constructor for OldSeqwareException.

OldSeqwareException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException

Constructor for OldSeqwareException.

onSubmit(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController

Handles the user's request to submit a new study.

onSubmit(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class net.sourceforge.solexatools.webapp.controller.LoginController

OOZIE_BATCH_SIZE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieProvisionFileJob

Determines size of buckets to use when batching provision file events

OOZIE_BATCH_THRESHOLD - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieProvisionFileJob

When the number of provision file events rooted at a job or in the workflow as a whole is above this threshold, start to use buckets

Oozie_Check - Class in io.seqware.pipeline.plugins.sanity.checks

Ensures that oozie is working by connecting to oozie url and checking the response code

Oozie_Check() - Constructor for class io.seqware.pipeline.plugins.sanity.checks.Oozie_Check

OOZIE_RETRY_INTERVAL - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob

OOZIE_RETRY_MAX - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob

oozie_working_dir - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

OozieBashJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object

OozieBashJob(AbstractJob, String, String, boolean, File, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob

OozieJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object

OozieJob(AbstractJob, String, String, boolean, File, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

OozieProvisionFileJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object

OozieProvisionFileJob(AbstractJob, SqwFile, String, String, boolean, File, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob

OozieWorkflowEngine - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie

OozieWorkflowEngine(AbstractWorkflowDataModel, boolean, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine

OozieWorkflowXmlGenerator - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie

OozieWorkflowXmlGenerator() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowXmlGenerator

OozieXML2Dot - Class in net.sourceforge.seqware.pipeline.plugins

OozieXML2Dot() - Constructor for class net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot

OpenInvoiceController - Class in net.sourceforge.solexatools.webapp.controller

OpenInvoiceController class.

OpenInvoiceController() - Constructor for class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController

Constructor for OpenInvoiceController.

OptionParsing - Class in net.sourceforge.seqware.common.util.configtools

Created by IntelliJ IDEA.

OptionParsing() - Constructor for class net.sourceforge.seqware.common.util.configtools.OptionParsing

options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory

options - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin

optsFileName(String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

Organism - Class in io.seqware.webservice.generated.model

Organism() - Constructor for class io.seqware.webservice.generated.model.Organism

Organism(Integer) - Constructor for class io.seqware.webservice.generated.model.Organism

Organism(Integer, String) - Constructor for class io.seqware.webservice.generated.model.Organism

Organism - Class in net.sourceforge.seqware.common.model

Organism class.

Organism() - Constructor for class net.sourceforge.seqware.common.model.Organism

Constructor for Organism.

OrganismDAO - Interface in net.sourceforge.seqware.common.dao

OrganismDAO interface.

OrganismDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

OrganismDAOHibernate class.

OrganismDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate

Constructor for OrganismDAOHibernate.

OrganismDto - Class in net.sourceforge.seqware.webservice.dto

OrganismDto() - Constructor for class net.sourceforge.seqware.webservice.dto.OrganismDto

OrganismFacadeREST - Class in io.seqware.webservice.generated.controller

OrganismFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.OrganismFacadeREST

OrganismList - Class in net.sourceforge.seqware.common.model.lists

OrganismList class.

OrganismList() - Constructor for class net.sourceforge.seqware.common.model.lists.OrganismList

Constructor for OrganismList.

OrganismResource - Class in net.sourceforge.seqware.webservice.resources.tables

ExperimentResource class.

OrganismResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.OrganismResource

Constructor for ExperimentResource.

OrganismService - Interface in net.sourceforge.seqware.common.business

OrganismService interface.

OrganismServiceImpl - Class in net.sourceforge.seqware.common.business.impl

OrganismServiceImpl class.

OrganismServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl

Constructor for OrganismServiceImpl.

originalFileName - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

OrphanCheckerPlugin - Class in net.sourceforge.seqware.pipeline.plugins.checkdb.plugins

Checks the metadb for orphans that are not connected to any other entities.

OrphanCheckerPlugin() - Constructor for class net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.OrphanCheckerPlugin

outputDir - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle

outputDir - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

outputLogString(boolean, WorkflowRunReportRow, StringBuilder) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource

outputLogString.

outputSize - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

outputZip - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle

OwnerDto - Class in net.sourceforge.seqware.webservice.dto

OwnerDto() - Constructor for class net.sourceforge.seqware.webservice.dto.OwnerDto

P

packageBundle(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

packageBundle.

packageBundleToS3(File, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

packageBundleToS3.

PAGE_NUM - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant PAGE_NUM="page"

PAGE_NUM - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant PAGE_NUM="page"

PageInfo - Class in net.sourceforge.solexatools.util

PageInfo class.

PageInfo() - Constructor for class net.sourceforge.solexatools.util.PageInfo

Constructor for PageInfo.

PaginationUtil - Class in net.sourceforge.solexatools.util

PaginationUtil class.

PaginationUtil() - Constructor for class net.sourceforge.solexatools.util.PaginationUtil

parameters - Variable in class net.sourceforge.seqware.common.module.ReturnValue

params - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin

PARENT_SAMPLE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant PARENT_SAMPLE_ATTRIBUTES="Header.PARENT_SAMPLE_ATTRIBUTES.getTitl"{trunked}

PARENT_SAMPLE_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant PARENT_SAMPLE_NAME="Header.PARENT_SAMPLE_NAME.getTitle()"

PARENT_SAMPLE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant PARENT_SAMPLE_SWA="Header.PARENT_SAMPLE_SWA.getTitle()"

PARENT_SAMPLE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant PARENT_SAMPLE_TAG_PREFIX="Header.PARENT_SAMPLE_TAG_PREFIX.getTitl"{trunked}

parentAccessionFiles - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

parentAccessionFiles - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

ParentAccessionModel - Interface in net.sourceforge.seqware.common.model

This links together all models that can be used to resolve a parent accession

parentAccessions - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

parentAccessions - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

parents - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

parse(String) - Static method in class net.sourceforge.seqware.common.util.Bool

Like Boolean.parseBoolean(String), but also yields true for case-insensitive values: "yes", "Y", "T"

parse(String) - Static method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerParser

parse(String, char) - Static method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerParser

parse_parameters() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface

Parameter validation code goes here.

parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin

Parameter validation code goes here.

parse_parameters() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface

Parameter validation code goes here.

parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld

Parameter validation code goes here.

parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin

Parameter validation code goes here.

parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner

parse_parameters.

parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin

Parameter validation code goes here.

parseClientInt(String) - Static method in class net.sourceforge.seqware.webservice.resources.BasicResource

Parses the ID field and throws resourceExceptions as needed

parsedFrom() - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo

parseFields() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

parseFiles() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

parseFromFile(File) - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo

parseFromFile.

parseMetaInfo(File) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility

Locate and parse metadata information and return a map representation

parseMiseqData(BufferedReader) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.ParseMiseqFile

ParseMiseqFile - Class in net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection

ParseMiseqFile(Metadata, Map<String, String>, boolean) - Constructor for class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.ParseMiseqFile

parseMiseqFile(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.ParseMiseqFile

parseMiseqHeader(BufferedReader, File) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.ParseMiseqFile

parseOption(Object, List<String>) - Static method in class net.sourceforge.seqware.common.util.configtools.OptionParsing

parseOption.

parseParentAccessions() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

parseParentAccessions(Map<String, String>) - Static method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

reads a map and tries to find the parent accessions, the result is de-duplicated.

parsePegasusStatus(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools

parsePegasusStatus.

parser - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin

parseXml(AbstractWorkflowDataModel, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowXmlParser

parse the FTL to XML, and XML to Java

pasteHtmlIntoParentNode(String, String, String, boolean) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil

pasteHtmlIntoParentNode.

PegasusJavaJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object

PegasusJavaJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJavaJob

PegasusJavaSeqwareModuleJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object

PegasusJavaSeqwareModuleJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJavaSeqwareModuleJob

PegasusJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object

a pegasusjob object and its subclasses match to the element in a dax

PegasusJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

PegasusPerlJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object

PegasusPerlJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusPerlJob

PegasusWorkflowEngine - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus

PegasusWorkflowEngine() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine

percentage - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools

percentage - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

PerlJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model

PerlJob(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.PerlJob

permanentBundleLocation - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle

PermissionsAware - Class in net.sourceforge.seqware.common.security

PermissionsAware interface.

PermissionsAware() - Constructor for class net.sourceforge.seqware.common.security.PermissionsAware

Pfn - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object

Pfn() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn

Platform - Class in io.seqware.webservice.generated.model

Platform() - Constructor for class io.seqware.webservice.generated.model.Platform

Platform(Integer) - Constructor for class io.seqware.webservice.generated.model.Platform

Platform - Class in net.sourceforge.seqware.common.model

Platform class.

Platform() - Constructor for class net.sourceforge.seqware.common.model.Platform

Constructor for Platform.

PlatformDAO - Interface in net.sourceforge.seqware.common.dao

PlatformDAO interface.

PlatformDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

PlatformDAOHibernate class.

PlatformDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate

Constructor for PlatformDAOHibernate.

PlatformFacadeREST - Class in io.seqware.webservice.generated.controller

PlatformFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.PlatformFacadeREST

PlatformList - Class in net.sourceforge.seqware.common.model.lists

PlatformList class.

PlatformList() - Constructor for class net.sourceforge.seqware.common.model.lists.PlatformList

Constructor for PlatformList.

PlatformResource - Class in net.sourceforge.seqware.webservice.resources.tables

ExperimentResource class.

PlatformResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.PlatformResource

Constructor for ExperimentResource.

PlatformService - Interface in net.sourceforge.seqware.common.business

PlatformService interface.

PlatformServiceImpl - Class in net.sourceforge.seqware.common.business.impl

PlatformServiceImpl class.

PlatformServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl

Constructor for PlatformServiceImpl.

Plugin - Class in net.sourceforge.seqware.pipeline.plugin

Abstract Plugin class.

Plugin() - Constructor for class net.sourceforge.seqware.pipeline.plugin.Plugin

Constructor for Plugin.

PluginInterface - Interface in net.sourceforge.seqware.pipeline.plugin

PluginInterface interface.

PluginRunner - Class in net.sourceforge.seqware.pipeline.runner

PluginRunner class.

PluginRunner() - Constructor for class net.sourceforge.seqware.pipeline.runner.PluginRunner

position - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

post(Representation) - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter

post(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessResource

postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource

postJaxb.

postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileResource

postJaxb.

postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.IusResource

postJaxb.

postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneResource

postJaxb.

postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessResource

postJaxb.

postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleResource

postJaxb.

postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource

postJaxb.

postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource

postJaxb.

postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource

postJaxb.

postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource

postJaxb.

postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowResource

postJaxb.

postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource

postJaxb.

postRun(Representation) - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter

postRun.

prepare(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

Validates and potentially modifies the specified model in preparation for launching.

prepareData(WorkflowInfo, String, ArrayList<String>, Map<String, String>, boolean, ArrayList<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

prepareData.

prepareWorkflow(AbstractWorkflowDataModel) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine

Prepare the workflow according to the info filled in the input objectModel.

prepareWorkflow(AbstractWorkflowDataModel) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine

prepareWorkflow(AbstractWorkflowDataModel) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine

prependToFilePath(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata

prettyPrint(Document, OutputStream) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools

prettyPrint(String) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools

prettyPrint.

prettyPrintString(Document) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools

prettyPrintString(String) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools

print(Writer, ReturnValue, String, boolean, FileMetadata) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

print(Writer, ReturnValue, String, boolean, FileMetadata, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Prints a line to the Excel spreadsheet.

print(String) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin

print.

print(Appendable, Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

print(Appendable, Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

print(Appendable, Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

print(String) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

print.

printAndAppendtoStderr(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue

printAndAppendtoStderr.

printAndAppendtoStderr(String) - Method in class net.sourceforge.seqware.pipeline.runner.Runner

printAndAppendtoStderr.

printAndAppendtoStdout(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue

printAndAppendtoStdout.

printAndAppendtoStdout(String) - Method in class net.sourceforge.seqware.pipeline.runner.Runner

printAndAppendtoStdout.

printAndAppendtoString(String, String) - Static method in class net.sourceforge.seqware.common.util.processtools.stderr.StdErr

printAndAppendtoString.

printf(String, Object...) - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

printFileMetadata(ReturnValue, FileMetadata) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

printHeader(Writer, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

printHeader(Writer, boolean, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Print the header of the Excel spreadsheet to file.

printLaneInfo(LaneInfo, Appendable) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

println(String) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin

println.

printRunInfo(RunInfo, Appendable) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

printSampleInfo(SampleInfo, Appendable) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

printTSVFile(Writer, boolean, List<ReturnValue>, String) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

printTSVFile(Writer, boolean, List<ReturnValue>, String, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

printTSVFile.

processExitStatus - Variable in class net.sourceforge.seqware.common.module.ReturnValue

ProcessIdProcessResource - Class in net.sourceforge.seqware.webservice.resources.queries

ProcessIdProcessResource class.

ProcessIdProcessResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.ProcessIdProcessResource

Constructor for ProcessIdProcessResource.

ProcessIDResource - Class in net.sourceforge.seqware.webservice.resources.tables

ProcessIDResource class.

ProcessIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource

Constructor for ProcessIDResource.

ProcessIDResource.IntListByName - Class in net.sourceforge.seqware.webservice.resources.tables

ProcessIDResource.IntListByName(String) - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource.IntListByName

Processing - Class in io.seqware.webservice.generated.model

Processing() - Constructor for class io.seqware.webservice.generated.model.Processing

Processing(Integer) - Constructor for class io.seqware.webservice.generated.model.Processing

Processing(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.Processing

Processing - Class in net.sourceforge.seqware.common.model

Processing() - Constructor for class net.sourceforge.seqware.common.model.Processing

Constructor for Processing.

PROCESSING - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant PROCESSING=100

PROCESSING_ALGO - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant PROCESSING_ALGO="Header.PROCESSING_ALGO.getTitle()"

PROCESSING_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant PROCESSING_ATTRIBUTES="Header.PROCESSING_ATTRIBUTES.getTitle()"

PROCESSING_DATE - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant PROCESSING_DATE="Header.PROCESSING_DATE.getTitle()"

processing_event_to_task_group(int, int[], int[], String, String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

processing_event_to_task_group.

processing_event_to_task_group(int, int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

processing_event_to_task_group.

processing_event_to_task_group(int, int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

processing_event_to_task_group.

processing_event_to_task_group(int, int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

processing_event_to_task_group.

PROCESSING_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant

Constant PROCESSING_PREFIX="ae_"

PROCESSING_SWID - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant PROCESSING_SWID="Header.PROCESSING_SWID.getTitle()"

PROCESSING_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant PROCESSING_TAG_PREFIX="Header.PROCESSING_TAG_PREFIX.getTitle()"

processingAccession - Variable in class net.sourceforge.seqware.pipeline.module.Module

ProcessingAttribute - Class in io.seqware.webservice.generated.model

ProcessingAttribute() - Constructor for class io.seqware.webservice.generated.model.ProcessingAttribute

ProcessingAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.ProcessingAttribute

ProcessingAttribute - Class in net.sourceforge.seqware.common.model

ProcessingAttribute generated by hbm2java

ProcessingAttribute() - Constructor for class net.sourceforge.seqware.common.model.ProcessingAttribute

Constructor for ProcessingAttribute.

ProcessingAttribute(int, Processing) - Constructor for class net.sourceforge.seqware.common.model.ProcessingAttribute

Constructor for ProcessingAttribute.

ProcessingAttribute(int, Processing, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.ProcessingAttribute

Constructor for ProcessingAttribute.

ProcessingAttributeDAO - Interface in net.sourceforge.seqware.common.dao

ProcessingAttributeDAO interface.

ProcessingAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ProcessingAttributeDAOHibernate class.

ProcessingAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate

ProcessingAttributeFacadeREST - Class in io.seqware.webservice.generated.controller

ProcessingAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ProcessingAttributeFacadeREST

ProcessingController - Class in net.sourceforge.solexatools.webapp.controller

SequencerRunController

ProcessingController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ProcessingController

Constructor for ProcessingController.

ProcessingController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.ProcessingController

Constructor for ProcessingController.

ProcessingDAO - Interface in net.sourceforge.seqware.common.dao

ProcessingDAO interface.

ProcessingDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ProcessingDAOHibernate class.

ProcessingDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

Constructor for ProcessingDAOHibernate.

ProcessingDataStructure2Dot - Class in net.sourceforge.seqware.pipeline.plugins

ProcessingDataStructure2Dot() - Constructor for class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot

ProcessingExperiments - Class in io.seqware.webservice.generated.model

ProcessingExperiments() - Constructor for class io.seqware.webservice.generated.model.ProcessingExperiments

ProcessingExperiments(Integer) - Constructor for class io.seqware.webservice.generated.model.ProcessingExperiments

ProcessingExperiments - Class in net.sourceforge.seqware.common.model

ProcessingExperiments generated by hbm2java

ProcessingExperiments() - Constructor for class net.sourceforge.seqware.common.model.ProcessingExperiments

Constructor for ProcessingExperiments.

ProcessingExperiments(int, Processing, Experiment) - Constructor for class net.sourceforge.seqware.common.model.ProcessingExperiments

Constructor for ProcessingExperiments.

ProcessingExperiments(int, Processing, Experiment, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingExperiments

Constructor for ProcessingExperiments.

ProcessingExperimentsDAO - Interface in net.sourceforge.seqware.common.dao

ProcessingExperimentsDAO interface.

ProcessingExperimentsDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ProcessingExperimentsDAOHibernate class.

ProcessingExperimentsDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate

ProcessingExperimentsFacadeREST - Class in io.seqware.webservice.generated.controller

ProcessingExperimentsFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ProcessingExperimentsFacadeREST

ProcessingExperimentsService - Interface in net.sourceforge.seqware.common.business

ProcessingExperimentsService interface.

ProcessingExperimentsServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ProcessingExperimentsServiceImpl class.

ProcessingExperimentsServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl

ProcessingFacadeREST - Class in io.seqware.webservice.generated.controller

ProcessingFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ProcessingFacadeREST

ProcessingFiles - Class in io.seqware.webservice.generated.model

ProcessingFiles() - Constructor for class io.seqware.webservice.generated.model.ProcessingFiles

ProcessingFiles(Integer) - Constructor for class io.seqware.webservice.generated.model.ProcessingFiles

ProcessingFilesFacadeREST - Class in io.seqware.webservice.generated.controller

ProcessingFilesFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ProcessingFilesFacadeREST

ProcessingIus - Class in io.seqware.webservice.generated.model

ProcessingIus() - Constructor for class io.seqware.webservice.generated.model.ProcessingIus

ProcessingIus(Integer) - Constructor for class io.seqware.webservice.generated.model.ProcessingIus

ProcessingIus - Class in net.sourceforge.seqware.common.model

ProcessingIus generated by hbm2java

ProcessingIus() - Constructor for class net.sourceforge.seqware.common.model.ProcessingIus

Constructor for ProcessingIus.

ProcessingIus(int, IUS, Processing) - Constructor for class net.sourceforge.seqware.common.model.ProcessingIus

Constructor for ProcessingIus.

ProcessingIus(int, IUS, Processing, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingIus

Constructor for ProcessingIus.

ProcessingIUSDAO - Interface in net.sourceforge.seqware.common.dao

ProcessingIUSDAO interface.

ProcessingIUSDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ProcessingIUSDAOHibernate class.

ProcessingIUSDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate

ProcessingIusFacadeREST - Class in io.seqware.webservice.generated.controller

ProcessingIusFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ProcessingIusFacadeREST

ProcessingIUSService - Interface in net.sourceforge.seqware.common.business

ProcessingIUSService interface.

ProcessingIUSServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ProcessingIUSServiceImpl class.

ProcessingIUSServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl

ProcessingLanes - Class in io.seqware.webservice.generated.model

ProcessingLanes() - Constructor for class io.seqware.webservice.generated.model.ProcessingLanes

ProcessingLanes(Integer) - Constructor for class io.seqware.webservice.generated.model.ProcessingLanes

ProcessingLanes - Class in net.sourceforge.seqware.common.model

ProcessingLanes generated by hbm2java

ProcessingLanes() - Constructor for class net.sourceforge.seqware.common.model.ProcessingLanes

Constructor for ProcessingLanes.

ProcessingLanes(int, Processing, Lane) - Constructor for class net.sourceforge.seqware.common.model.ProcessingLanes

Constructor for ProcessingLanes.

ProcessingLanes(int, Processing, Lane, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingLanes

Constructor for ProcessingLanes.

ProcessingLanesDAO - Interface in net.sourceforge.seqware.common.dao

ProcessingLanesDAO interface.

ProcessingLanesDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ProcessingLanesDAOHibernate class.

ProcessingLanesDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate

ProcessingLanesFacadeREST - Class in io.seqware.webservice.generated.controller

ProcessingLanesFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ProcessingLanesFacadeREST

ProcessingLanesService - Interface in net.sourceforge.seqware.common.business

ProcessingLanesService interface.

ProcessingLanesServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ProcessingLanesServiceImpl class.

ProcessingLanesServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl

ProcessingList - Class in net.sourceforge.seqware.common.model.lists

ProcessingList class.

ProcessingList() - Constructor for class net.sourceforge.seqware.common.model.lists.ProcessingList

Constructor for ProcessingList.

ProcessingRelationship - Class in io.seqware.webservice.generated.model

ProcessingRelationship() - Constructor for class io.seqware.webservice.generated.model.ProcessingRelationship

ProcessingRelationship(Integer) - Constructor for class io.seqware.webservice.generated.model.ProcessingRelationship

ProcessingRelationship - Class in net.sourceforge.seqware.common.model

ProcessingRelationship generated by hbm2java

ProcessingRelationship() - Constructor for class net.sourceforge.seqware.common.model.ProcessingRelationship

Constructor for ProcessingRelationship.

ProcessingRelationship(int) - Constructor for class net.sourceforge.seqware.common.model.ProcessingRelationship

Constructor for ProcessingRelationship.

ProcessingRelationship(int, Processing, Processing, String) - Constructor for class net.sourceforge.seqware.common.model.ProcessingRelationship

Constructor for ProcessingRelationship.

ProcessingRelationshipDAO - Interface in net.sourceforge.seqware.common.dao

ProcessingRelationshipDAO interface.

ProcessingRelationshipDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ProcessingRelationshipDAOHibernate class.

ProcessingRelationshipDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate

ProcessingRelationshipFacadeREST - Class in io.seqware.webservice.generated.controller

ProcessingRelationshipFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ProcessingRelationshipFacadeREST

ProcessingRelationshipService - Interface in net.sourceforge.seqware.common.business

ProcessingRelationshipService interface.

ProcessingRelationshipServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ProcessingRelationshipServiceImpl class.

ProcessingRelationshipServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl

ProcessingSamples - Class in io.seqware.webservice.generated.model

ProcessingSamples() - Constructor for class io.seqware.webservice.generated.model.ProcessingSamples

ProcessingSamples(Integer) - Constructor for class io.seqware.webservice.generated.model.ProcessingSamples

ProcessingSamples - Class in net.sourceforge.seqware.common.model

ProcessingSamples generated by hbm2java

ProcessingSamples() - Constructor for class net.sourceforge.seqware.common.model.ProcessingSamples

Constructor for ProcessingSamples.

ProcessingSamples(int, Processing, Sample) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSamples

Constructor for ProcessingSamples.

ProcessingSamples(int, Processing, Sample, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSamples

Constructor for ProcessingSamples.

ProcessingSamplesDAO - Interface in net.sourceforge.seqware.common.dao

ProcessingSamplesDAO interface.

ProcessingSamplesDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ProcessingSamplesDAOHibernate class.

ProcessingSamplesDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate

ProcessingSamplesFacadeREST - Class in io.seqware.webservice.generated.controller

ProcessingSamplesFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ProcessingSamplesFacadeREST

ProcessingSamplesService - Interface in net.sourceforge.seqware.common.business

ProcessingSamplesService interface.

ProcessingSamplesServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ProcessingSamplesServiceImpl class.

ProcessingSamplesServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl

processingsCount(Sample) - Static method in class net.sourceforge.solexatools.util.TagUtils

Returns count of the Sample related Workflow Runs.

ProcessingSequencerRuns - Class in io.seqware.webservice.generated.model

ProcessingSequencerRuns() - Constructor for class io.seqware.webservice.generated.model.ProcessingSequencerRuns

ProcessingSequencerRuns(Integer) - Constructor for class io.seqware.webservice.generated.model.ProcessingSequencerRuns

ProcessingSequencerRuns - Class in net.sourceforge.seqware.common.model

ProcessingSequencerRuns generated by hbm2java

ProcessingSequencerRuns() - Constructor for class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Constructor for ProcessingSequencerRuns.

ProcessingSequencerRuns(int, Processing, SequencerRun) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Constructor for ProcessingSequencerRuns.

ProcessingSequencerRuns(int, Processing, SequencerRun, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Constructor for ProcessingSequencerRuns.

ProcessingSequencerRunsDAO - Interface in net.sourceforge.seqware.common.dao

ProcessingSequencerRunsDAO interface.

ProcessingSequencerRunsDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ProcessingSequencerRunsDAOHibernate class.

ProcessingSequencerRunsDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate

ProcessingSequencerRunsFacadeREST - Class in io.seqware.webservice.generated.controller

ProcessingSequencerRunsFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ProcessingSequencerRunsFacadeREST

ProcessingSequencerRunsService - Interface in net.sourceforge.seqware.common.business

ProcessingSequencerRunsService interface.

ProcessingSequencerRunsServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ProcessingSequencerRunsServiceImpl class.

ProcessingSequencerRunsServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl

ProcessingService - Interface in net.sourceforge.seqware.common.business

ProcessingService interface.

ProcessingServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ProcessingServiceImpl class.

ProcessingServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

Constructor for ProcessingServiceImpl.

ProcessingSetupController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController

ProcessingSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController

Constructor for ProcessingSetupController.

ProcessingStatus - Enum in net.sourceforge.seqware.common.model

ProcessingStructureResource - Class in net.sourceforge.seqware.webservice.resources.tables

ProcessingStructureResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ProcessingStructureResource

ProcessingStudies - Class in io.seqware.webservice.generated.model

ProcessingStudies() - Constructor for class io.seqware.webservice.generated.model.ProcessingStudies

ProcessingStudies(Integer) - Constructor for class io.seqware.webservice.generated.model.ProcessingStudies

ProcessingStudies - Class in net.sourceforge.seqware.common.model

ProcessingStudies generated by hbm2java

ProcessingStudies() - Constructor for class net.sourceforge.seqware.common.model.ProcessingStudies

Constructor for ProcessingStudies.

ProcessingStudies(int, Processing, Study) - Constructor for class net.sourceforge.seqware.common.model.ProcessingStudies

Constructor for ProcessingStudies.

ProcessingStudies(int, Processing, Study, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingStudies

Constructor for ProcessingStudies.

ProcessingStudiesDAO - Interface in net.sourceforge.seqware.common.dao

ProcessingStudiesDAO interface.

ProcessingStudiesDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ProcessingStudiesDAOHibernate class.

ProcessingStudiesDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate

ProcessingStudiesFacadeREST - Class in io.seqware.webservice.generated.controller

ProcessingStudiesFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ProcessingStudiesFacadeREST

ProcessingStudiesService - Interface in net.sourceforge.seqware.common.business

ProcessingStudiesService interface.

ProcessingStudiesServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ProcessingStudiesServiceImpl class.

ProcessingStudiesServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl

processOutput(SortedMap<CheckDBPluginInterface.Level, Set<String>>, CheckDBPluginInterface.Level, String, List<Integer>) - Static method in class net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB

Convenience method for processing output and appending it to the warning map

ProcessResource - Class in net.sourceforge.seqware.webservice.resources.tables

ProcessResource class.

ProcessResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ProcessResource

Constructor for ProcessResource.

processTemplate(String[], String, String, Map<String, String>, String[]) - Method in class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator

processTemplate.

ProcessTools - Class in net.sourceforge.seqware.common.util.processtools

Sleep for N seconds.

ProcessTools() - Constructor for class net.sourceforge.seqware.common.util.processtools.ProcessTools

PROGRAMFAILED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant PROGRAMFAILED=1

promptAccession(String, int, BatchMetadataParser.KeyVal[], BatchMetadataParser.Field) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

promptBoolean(String, Boolean) - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

promptBoolean(String, Boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

promptForExperiment(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

promptForFields(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

promptForIUS(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

promptForLane(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

promptForSample(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

promptForSequencerRun(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

promptForStudy(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

promptInteger(String, Integer) - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

promptInteger(String, int, BatchMetadataParser.Field) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

promptInteger(String, Integer) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

promptPositiveInteger(String, int, BatchMetadataParser.Field, int, int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

promptString(String, String) - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

promptString(String, String, BatchMetadataParser.Field) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

promptString(String, String, String[], String, BatchMetadataParser.Field) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

Determine a value for a field 'title' of sample 'sampleName'.

promptString(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata

PropagateOwnership - Class in net.sourceforge.seqware.common.hibernate

Should only be used for one query and then discarded and re-instantiated.

PropagateOwnership() - Constructor for class net.sourceforge.seqware.common.hibernate.PropagateOwnership

Constructor for PropagateOwnership.

ProvenanceUtility - Class in net.sourceforge.seqware.pipeline.plugins.fileprovenance

Convenience methods that can be shared by utilities that access the FileProvenance report

ProvenanceUtility() - Constructor for class net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility

ProvenanceUtility.HumanProvenanceFilters - Enum in net.sourceforge.seqware.pipeline.plugins.fileprovenance

provideBundleDir(Map<String, String>, String) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools

ProvidedBundleCLIUserPhase5 - Class in io.seqware.pipeline.plugins.sanity

Build and install a bundle, used by both the User tutorial and the Developer tutorial

ProvidedBundleCLIUserPhase5() - Constructor for class io.seqware.pipeline.plugins.sanity.ProvidedBundleCLIUserPhase5

ProvidedBundleUserPhase5 - Class in io.seqware.pipeline.plugins.sanity

Build and install a bundle, used by both the User tutorial and the Developer tutorial

ProvidedBundleUserPhase5() - Constructor for class io.seqware.pipeline.plugins.sanity.ProvidedBundleUserPhase5

providedMap(String) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools

ProvisionDependenciesBundle - Class in net.sourceforge.seqware.pipeline.modules.utilities

Purpose: This module takes a software bundle and unzips it to the temporary directory.

ProvisionDependenciesBundle() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle

provisionFile(String, String, boolean, ArrayList<FileMetadata>, boolean) - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

provisionFile.

ProvisionFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities

Purpose: This module takes one or more inputs (S3 URL, HTTP/HTTPS URL, or local file path) and copies the file to the specified output (S3 bucket URL, HTTP/HTTPS URL, or local directory path).

ProvisionFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

ProvisionFilesJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object

ProvisionFilesJob(AbstractJob, String, SqwFile, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob

ProvisionFilesUtil - Class in net.sourceforge.seqware.common.util.filetools

ProvisionFilesUtil class.

ProvisionFilesUtil() - Constructor for class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Default ctor.

ProvisionFilesUtil(boolean) - Constructor for class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Set verbose mode ctor.

put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource

put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource

put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource

put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileIDResource

put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.IusIDResource

put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneIDResource

put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource

put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource

put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource

put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource

put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource

put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource

put(HttpServletRequest) - Static method in class net.sourceforge.solexatools.Debug

put.

put(String) - Static method in class net.sourceforge.solexatools.Debug

put.

put(Object, String) - Static method in class net.sourceforge.solexatools.Debug

put.

putDestination(BufferedInputStream, String, int, String, ArrayList<FileMetadata>, boolean) - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

HTTP writeback currently not supported S3 uses multi-part upload which should deal with failed uploads (maybe) I'm not really dealing with failed upload recovery here...

putToHttp() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Not supported yet.

putToS3(BufferedInputStream, String, boolean) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Copy file using reader into output.

putToS3(BufferedInputStream, String, boolean, int, int, int, int) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

putToS3(InputStream, String, boolean, Cipher, Cipher) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Copy file using reader into output.

putToS3(InputStream, String, boolean, int, int, int, int, Cipher, Cipher) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Q

queryMap(Request) - Static method in class net.sourceforge.seqware.webservice.resources.BasicRestlet

QueryRunner - Class in io.seqware.pipeline.plugins.sanity

A class that allows plugin writers to do queries

QueryRunner(MetadataDB) - Constructor for class io.seqware.pipeline.plugins.sanity.QueryRunner

queryValues - Variable in class net.sourceforge.seqware.webservice.resources.BasicResource

queryValues - Variable in class net.sourceforge.seqware.webservice.resources.BasicRestlet

QUEUED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant QUEUED=101

R

random - Variable in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

RandomInvitationCode - Class in net.sourceforge.seqware.common.invitation

RandomInvitationCode class.

RandomInvitationCode() - Constructor for class net.sourceforge.seqware.common.invitation.RandomInvitationCode

Constructor for RandomInvitationCode.

RandomInvitationCode - Class in net.sourceforge.solexatools.util

RandomInvitationCode class.

RandomInvitationCode() - Constructor for class net.sourceforge.solexatools.util.RandomInvitationCode

Constructor for RandomInvitationCode.

READ_ATTEMPTS - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

reader() - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

readLine() - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

readLine(String, Object...) - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

readPassword() - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

readPassword(String, Object...) - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

recursivelyUploadDir(String, String, String, TransferManager) - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory

RedirectAware - Interface in net.sourceforge.seqware.pipeline.module

This module, in conjunction with the Tag and Run annotation are used to replace the old Module with the Runner code.

Registration - Class in io.seqware.webservice.generated.model

Registration() - Constructor for class io.seqware.webservice.generated.model.Registration

Registration(Integer) - Constructor for class io.seqware.webservice.generated.model.Registration

Registration(Integer, String, String, String, boolean, Date, Date, boolean, boolean, boolean) - Constructor for class io.seqware.webservice.generated.model.Registration

Registration - Class in net.sourceforge.seqware.common.model

Registration

Registration() - Constructor for class net.sourceforge.seqware.common.model.Registration

Constructor for Registration.

registration - Variable in class net.sourceforge.seqware.webservice.resources.BasicResource

registration - Variable in class net.sourceforge.seqware.webservice.resources.BasicRestlet

RegistrationController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationController class.

RegistrationController() - Constructor for class net.sourceforge.solexatools.webapp.controller.RegistrationController

Constructor for RegistrationController.

RegistrationController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.RegistrationController

Constructor for RegistrationController.

RegistrationDAO - Interface in net.sourceforge.seqware.common.dao

RegistrationDAO interface.

RegistrationDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

RegistrationDAOHibernate class.

RegistrationDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate

Constructor for RegistrationDAOHibernate.

RegistrationDTO - Class in net.sourceforge.seqware.common.model

RegistrationDTO() - Constructor for class net.sourceforge.seqware.common.model.RegistrationDTO

Constructor for RegistrationDTO.

RegistrationFacadeREST - Class in io.seqware.webservice.generated.controller

RegistrationFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.RegistrationFacadeREST

RegistrationService - Interface in net.sourceforge.seqware.common.business

RegistrationService interface.

RegistrationServiceImpl - Class in net.sourceforge.seqware.common.business.impl

RegistrationServiceImpl class.

RegistrationServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl

Constructor for RegistrationServiceImpl.

RegistrationSetupController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp

RegistrationSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController

Constructor for RegistrationSetupController.

RegistrationValidator - Class in net.sourceforge.solexatools.validation

RegistrationValidator class.

RegistrationValidator() - Constructor for class net.sourceforge.solexatools.validation.RegistrationValidator

Constructor for RegistrationValidator.

release() - Static method in class net.sourceforge.seqware.pipeline.tools.RunLock

Releases a lock if one was acquired, otherwise no-op.

releaseLock() - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock

Deprecated.

releaseLock.

remove(String) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

remove(T) - Method in class io.seqware.webservice.generated.controller.AbstractFacade

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ExpenseAttributeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ExpenseFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentAttributeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentLibraryDesignFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentLinkFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignReadSpecFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.FileAttributeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.FileFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.FileReportFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.FileTypeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.InvoiceAttributeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.InvoiceFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.IusAttributeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.IusFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.IusLinkFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.IusWorkflowRunsFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.LaneAttributeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.LaneFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.LaneLinkFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.LaneTypeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.LaneWorkflowRunsFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.LibrarySelectionFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.LibrarySourceFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.LibraryStrategyFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.OrganismFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.PlatformFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingAttributeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingExperimentsFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingFilesFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingIusFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingLanesFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingRelationshipFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingSamplesFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingSequencerRunsFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ProcessingStudiesFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.RegistrationFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.SampleAttributeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.SampleFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.SampleLinkFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.SampleRelationshipFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.SampleReportFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.SampleSearchAttributeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.SampleSearchFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.SequencerRunAttributeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.SequencerRunFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ShareExperimentFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ShareFileFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ShareLaneFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ShareProcessingFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ShareSampleFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ShareStudyFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.ShareWorkflowRunFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.StudyAttributeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.StudyFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.StudyLinkFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.StudyTypeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowAttributeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowParamFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowParamValueFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowRunAttributeFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowRunFacadeREST

remove(Integer) - Method in class io.seqware.webservice.generated.controller.WorkflowRunParamFacadeREST

remove_rdelete(Class, String, Set<ModelAccessionIDTuple>) - Method in class io.seqware.webservice.client.SeqWareWebServiceClient

removeSelectedItemsCurrentParam(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

removeSelectedItemsCurrentParam.

removeSelectedItemsLaunchWorkflow(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

removeSelectedItemsLaunchWorkflow.

removeSequencerRun(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

removeSequencerRun.

removeStudy(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

removeStudy.

removeWorkflowRun(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

removeWorkflowRun.

removeWorkflowRunRunning(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

removeWorkflowRunRunning.

replace(String, String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.StringUtils

resolve all the FTL variables ${variable} in the string with the variables in maps

replace(String, Map<String, String>) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.StringUtils

replace.

reportLaunch() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

Report an actual launch of a workflow for testing purpose

reportLaunch() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin

Report an actual launch of a workflow for testing purpose

Reports - Class in io.seqware

Reports() - Constructor for class io.seqware.Reports

ReportTest - Class in net.sourceforge.seqware.pipeline.tools

ReportTest class.

ReportTest() - Constructor for class net.sourceforge.seqware.pipeline.tools.ReportTest

ReportTest.TestThread - Class in net.sourceforge.seqware.pipeline.tools

ReportTest.TestThread() - Constructor for class net.sourceforge.seqware.pipeline.tools.ReportTest.TestThread

represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.VersionResource

represent.

represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.WorkflowResource

represent.

represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.WorkflowRunStatusResource

represent.

Requirement - Class in net.sourceforge.seqware.pipeline.workflowV2.model

Requirement() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement

Requirement.Type - Enum in net.sourceforge.seqware.pipeline.workflowV2.model

enum of all Type

requireRegistration(HttpServletRequest, HttpServletResponse) - Static method in class net.sourceforge.solexatools.Security

requireRegistration.

requiresNewLauncher(Workflow) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility

requiresNewLauncher(String, String, String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility

requiresNewLauncher(OptionSet) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility

rerunWorkflowRun(Collection<String>, Collection<Integer>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

Returns true only if there are more files to run than have been run on any workflow so far, or if the filesToRun have different filepaths than those that have been run before.

ReservedIniKeys - Enum in net.sourceforge.seqware.common.util.maptools

This enum collects all reserved ini file keys that are reserved by SeqWare.

resetCompletedChildren() - Method in class net.sourceforge.seqware.common.model.Processing

resetCompletedChildren.

resetDatabaseWithUsers() - Static method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator

Unfortunately, postgres does not allow the straight dropdb and createdb when tomcat is used (perhaps we leave open a connection)

resetDatabaseWithUsers() - Static method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreatorWrapper

resetDatabaseWithUsers() - Static method in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator

Unfortunately, postgres does not allow the straight dropdb and createdb when tomcat is used (perhaps we leave open a connection)

resetRunningChildren() - Method in class net.sourceforge.seqware.common.model.Processing

resetRunningChildren.

resolveWorkflowBundleDirPath(File, String) - Static method in class net.sourceforge.seqware.pipeline.bundle.Bundle

ret - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle

ret - Variable in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

ret - Variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

ret - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

Rethrow - Class in net.sourceforge.seqware.common.util

Rethrow() - Constructor for class net.sourceforge.seqware.common.util.Rethrow

rethrow(Throwable) - Static method in class net.sourceforge.seqware.common.util.Rethrow

Rethrows t if unchecked, otherwise throws t wrapped in a RuntimeException.

retrieveCompiledSeqwareScript() - Static method in class net.sourceforge.seqware.pipeline.plugins.ITUtility

Grab the location of the compiled seqware script.

retrieveFullAssembledJar() - Static method in class net.sourceforge.seqware.pipeline.plugins.ITUtility

This is the hackiest hack in the universe of hacks for getting the final assembly jar so I can run tests.

RetryAnalysisWorkflowController - Class in net.sourceforge.solexatools.webapp.controller

RetryAnalysisWorkflowController class.

RetryAnalysisWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.RetryAnalysisWorkflowController

Constructor for RetryAnalysisWorkflowController.

RETURNEDHELPMSG - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant RETURNEDHELPMSG=110

ReturnValue - Class in net.sourceforge.seqware.common.module

Return values > 0 are errors that will cause the runner to exit.

ReturnValue() - Constructor for class net.sourceforge.seqware.common.module.ReturnValue

Constructor for ReturnValue.

ReturnValue(int) - Constructor for class net.sourceforge.seqware.common.module.ReturnValue

Constructor for ReturnValue.

ReturnValue(String, String, int) - Constructor for class net.sourceforge.seqware.common.module.ReturnValue

Constructor for ReturnValue.

returnValue - Variable in class net.sourceforge.seqware.common.module.ReturnValue

returnValue - Variable in class net.sourceforge.seqware.common.util.filetools.FileTools.LocalhostPair

ReturnValue.ExitStatus - Enum in net.sourceforge.seqware.common.module

ReturnValueList - Class in net.sourceforge.seqware.common.model.lists

ReturnValueList class.

ReturnValueList() - Constructor for class net.sourceforge.seqware.common.model.lists.ReturnValueList

Constructor for ReturnValueList.

RootSampleResource - Class in net.sourceforge.seqware.webservice.resources.tables

This resource should pull back only samples without parents

RootSampleResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.RootSampleResource

Constructor for RootSampleResource.

ROWS_PER_PAGE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant ROWS_PER_PAGE="rp"

ROWS_PER_PAGE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant ROWS_PER_PAGE="rp"

run() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread

run(String[]) - Method in class net.sourceforge.seqware.pipeline.runner.PluginRunner

run.

run(String[]) - Method in class net.sourceforge.seqware.pipeline.runner.Runner

run.

run() - Method in class net.sourceforge.seqware.pipeline.tools.ReportTest.TestThread

runArbitraryCommand(String, int, File) - Static method in class net.sourceforge.seqware.pipeline.plugins.ITUtility

Run an arbitrary command and check it against an expected return value

runCommand(Map<String, String>, String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools

runCommand.

runCommand(String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools

runCommand.

runCommand(String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools

runCommand.

runCommand(Map<String, String>, String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools

runCommand(Map<String, String>, String[], int, int) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools

A simple command runner that captures the return value of the program.

RunInfo - Class in net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection

RunInfo() - Constructor for class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

runInSessionCalculations() - Method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions

runInSessionCalculations.

RunLock - Class in net.sourceforge.seqware.pipeline.tools

Allows for preventing concurrent processes owned by the same user.

RunLock() - Constructor for class net.sourceforge.seqware.pipeline.tools.RunLock

Runner - Class in net.sourceforge.seqware.pipeline.runner

Runner class.

Runner() - Constructor for class net.sourceforge.seqware.pipeline.runner.Runner

Runner.Keys - Interface in net.sourceforge.seqware.pipeline.runner

RUNNERERR - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant RUNNERERR=91

runnerFileName(String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

runnerMetaDataArgs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

Returns the metadata arg list for the Runner.

runQuery(ResultSetHandler<T>, String, Object...) - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

Convenient method to run a query against the test database, avoids unclosed connections.

runQuery(ResultSetHandler<T>, String, boolean, Object...) - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

Convenient method to run a query against the test database, avoids unclosed connections.

runSeqwareCLI(String, int, File) - Static method in class net.sourceforge.seqware.pipeline.plugins.ITUtility

Run the new SeqWare simplified command-line script given a particular set of parameters and check for an expected return value.

runSeqWareJar(String, int, File) - Static method in class net.sourceforge.seqware.pipeline.plugins.ITUtility

Run the SeqWare jar given a particular set of parameters and check for an expected return value.

runStartTstmp - Variable in class net.sourceforge.seqware.common.module.ReturnValue

runStopTstmp - Variable in class net.sourceforge.seqware.common.module.ReturnValue

RUNTIMEEXCEPTION - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant RUNTIMEEXCEPTION=6

RunTools - Class in net.sourceforge.seqware.common.util.runtools

RunTools class.

RunTools() - Constructor for class net.sourceforge.seqware.common.util.runtools.RunTools

runUpdate(String, Object...) - Method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

Run an insert, update, or delete

runWorkflow(WorkflowInfo, String, String, boolean, String, ArrayList<String>, Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

runWorkflow.

runWorkflow(WorkflowInfo, String, String, boolean, String, ArrayList<String>, Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

runWorkflow.

runWorkflow(WorkflowInfo, String, String, boolean, String, ArrayList<String>, Registration) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager

runWorkflow.

runWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine

Run the prepared workflow.

runWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine

runWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine

RunWorkflowResource - Class in net.sourceforge.seqware.webservice.resources.queries

RunWorkflowResource class.

RunWorkflowResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.RunWorkflowResource

Constructor for RunWorkflowResource.

S

s3ConnectionTimeout - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

S3CreateFileURLs - Class in net.sourceforge.seqware.pipeline.modules.utilities

Purpose: This module simply lists files at the S3 URL you provide and creates temporary URLs that can be shared with others.

S3CreateFileURLs() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

S3DeleteFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities

Purpose: This module simply lists files at the S3 URL you provide.

S3DeleteFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

S3ListFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities

Purpose: This module simply lists files at the S3 URL you provide.

S3ListFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

s3MaxConnections - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

s3MaxErrorRetry - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

s3SocketTimeout - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

S3UploadDirectory - Class in net.sourceforge.seqware.pipeline.modules.utilities

Purpose: This module uses the Amazon API to recursively upload a directory to an S3 bucket.

S3UploadDirectory() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory

safe(String) - Static method in class net.sourceforge.seqware.common.util.Str

Returns a String suitable to be used in multiple contexts, e.g., as part of a filename.

Sample - Class in io.seqware.webservice.generated.model

Sample() - Constructor for class io.seqware.webservice.generated.model.Sample

Sample(Integer) - Constructor for class io.seqware.webservice.generated.model.Sample

Sample(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.Sample

Sample - Class in net.sourceforge.seqware.common.model

Sample() - Constructor for class net.sourceforge.seqware.common.model.Sample

Constructor for Sample.

SAMPLE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant SAMPLE_ATTRIBUTES="Header.SAMPLE_ATTRIBUTES.getTitle()"

SAMPLE_CHILD - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant SAMPLE_CHILD="s_child"

SAMPLE_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant SAMPLE_NAME="Header.SAMPLE_NAME.getTitle()"

SAMPLE_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant

Constant SAMPLE_PREFIX="sam_"

SAMPLE_SAMPLE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant SAMPLE_SAMPLE="s_sample"

SAMPLE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant SAMPLE_SWA="Header.SAMPLE_SWA.getTitle()"

SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController

Constant SAMPLE_SWID="sw"

SAMPLE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant SAMPLE_TAG_PREFIX="Header.SAMPLE_TAG_PREFIX.getTitle()"

SampleAttribute - Class in io.seqware.webservice.generated.model

SampleAttribute() - Constructor for class io.seqware.webservice.generated.model.SampleAttribute

SampleAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleAttribute

SampleAttribute(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.SampleAttribute

SampleAttribute - Class in net.sourceforge.seqware.common.model

SampleAttribute generated by hbm2java

SampleAttribute() - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute

Constructor for SampleAttribute.

SampleAttribute(int, Sample, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute

Constructor for SampleAttribute.

SampleAttribute(int, Sample, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute

Constructor for SampleAttribute.

sampleAttributeAsDto(SampleAttribute) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos

sampleAttributeAsDto.

SampleAttributeDAO - Interface in net.sourceforge.seqware.common.dao

SampleAttributeDAO interface.

SampleAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

SampleAttributeDAOHibernate class.

SampleAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate

SampleAttributeFacadeREST - Class in io.seqware.webservice.generated.controller

SampleAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleAttributeFacadeREST

SampleController - Class in net.sourceforge.solexatools.webapp.controller

SampleController

SampleController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleController

Constructor for SampleController.

SampleController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleController

Constructor for SampleController.

SampleDAO - Interface in net.sourceforge.seqware.common.dao

SampleDAO interface.

SampleDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

SampleDAOHibernate class.

SampleDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

Constructor for SampleDAOHibernate.

SampleDetailsLineItem - Class in net.sourceforge.solexatools.webapp.metamodel

SampleDetailsLineItem class.

SampleDetailsLineItem(SequencerRun, Lane, IUS) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem

Constructor for SampleDetailsLineItem.

SampleDetailsWorkflowLineItems - Class in net.sourceforge.solexatools.webapp.metamodel

SampleDetailsWorkflowLineItems class.

SampleDetailsWorkflowLineItems(Sample) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems

Constructor for SampleDetailsWorkflowLineItems.

SampleDetailsWorkflowLineItems(Processing) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems

Constructor for SampleDetailsWorkflowLineItems.

SampleFacadeREST - Class in io.seqware.webservice.generated.controller

SampleFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleFacadeREST

SampleHierarchies - Class in net.sourceforge.seqware.queryengine.webservice.model

SampleHierarchies() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchies

SampleHierarchy - Class in net.sourceforge.seqware.queryengine.webservice.model

SampleHierarchy() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy

SampleHierarchyPlugin - Class in net.sourceforge.seqware.pipeline.plugins.checkdb.plugins

Checks the metadb for issues specifically with the sample hierarchy.

SampleHierarchyPlugin() - Constructor for class net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.SampleHierarchyPlugin

SampleHierarchyResource - Class in net.sourceforge.seqware.webservice.resources.queries

SampleHierarchyResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SampleHierarchyResource

SampleIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries

SampleIdFilesResource class.

SampleIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SampleIdFilesResource

Constructor for SampleIdFilesResource.

SampleIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters

SampleIDFilter class.

SampleIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter

SampleIDResource - Class in net.sourceforge.seqware.webservice.resources.tables

SampleIDResource class.

SampleIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource

Constructor for SampleIDResource.

SampleInfo - Class in net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection

SampleInfo() - Constructor for class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

SampleLink - Class in io.seqware.webservice.generated.model

SampleLink() - Constructor for class io.seqware.webservice.generated.model.SampleLink

SampleLink(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleLink

SampleLink(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.SampleLink

SampleLink - Class in net.sourceforge.seqware.common.model

SampleLink generated by hbm2java

SampleLink() - Constructor for class net.sourceforge.seqware.common.model.SampleLink

Constructor for SampleLink.

SampleLink(int, Sample, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleLink

Constructor for SampleLink.

SampleLink(int, Sample, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleLink

Constructor for SampleLink.

SampleLinkDAO - Interface in net.sourceforge.seqware.common.dao

SampleLinkDAO interface.

SampleLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

SampleLinkDAOHibernate class.

SampleLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate

SampleLinkFacadeREST - Class in io.seqware.webservice.generated.controller

SampleLinkFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleLinkFacadeREST

SampleList - Class in net.sourceforge.seqware.common.model.lists

SampleList class.

SampleList() - Constructor for class net.sourceforge.seqware.common.model.lists.SampleList

Constructor for SampleList.

SampleRelationship - Class in io.seqware.webservice.generated.model

SampleRelationship() - Constructor for class io.seqware.webservice.generated.model.SampleRelationship

SampleRelationship(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleRelationship

SampleRelationshipFacadeREST - Class in io.seqware.webservice.generated.controller

SampleRelationshipFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleRelationshipFacadeREST

SampleReport - Class in io.seqware.webservice.generated.model

SampleReport() - Constructor for class io.seqware.webservice.generated.model.SampleReport

SampleReport(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleReport

SampleReportDAO - Interface in net.sourceforge.seqware.common.dao

SampleReportDAO interface.

SampleReportDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

SampleReportDAOHibernate class.

SampleReportDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate

SampleReportFacadeREST - Class in io.seqware.webservice.generated.controller

SampleReportFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleReportFacadeREST

SampleReportRow - Class in net.sourceforge.seqware.common.model

SampleReportRow class.

SampleReportRow() - Constructor for class net.sourceforge.seqware.common.model.SampleReportRow

SampleReportService - Interface in net.sourceforge.seqware.common.business

SampleReportService interface.

SampleReportService.Status - Enum in net.sourceforge.seqware.common.business

SampleReportServiceImpl - Class in net.sourceforge.seqware.common.business.impl

SampleReportServiceImpl class.

SampleReportServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

SampleResource - Class in net.sourceforge.seqware.webservice.resources.tables

SampleResource class.

SampleResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SampleResource

Constructor for SampleResource.

SampleSearch - Class in io.seqware.webservice.generated.model

SampleSearch() - Constructor for class io.seqware.webservice.generated.model.SampleSearch

SampleSearch(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleSearch

SampleSearch(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.SampleSearch

SampleSearch - Class in net.sourceforge.seqware.common.model

A search for samples that match a given list of attributes.

SampleSearch() - Constructor for class net.sourceforge.seqware.common.model.SampleSearch

SampleSearchAttribute - Class in io.seqware.webservice.generated.model

SampleSearchAttribute() - Constructor for class io.seqware.webservice.generated.model.SampleSearchAttribute

SampleSearchAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleSearchAttribute

SampleSearchAttribute(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.SampleSearchAttribute

SampleSearchAttribute - Class in net.sourceforge.seqware.common.model

Attributes that are part of a sample search.

SampleSearchAttribute() - Constructor for class net.sourceforge.seqware.common.model.SampleSearchAttribute

SampleSearchAttributeFacadeREST - Class in io.seqware.webservice.generated.controller

SampleSearchAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleSearchAttributeFacadeREST

SampleSearchDAO - Interface in net.sourceforge.seqware.common.dao

SampleSearchDAO interface.

SampleSearchDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

SampleSearchDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate

SampleSearchDto - Class in net.sourceforge.seqware.webservice.dto

SampleSearchDto() - Constructor for class net.sourceforge.seqware.webservice.dto.SampleSearchDto

SampleSearchFacadeREST - Class in io.seqware.webservice.generated.controller

SampleSearchFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleSearchFacadeREST

SampleSearchService - Interface in net.sourceforge.seqware.common.business

SampleSearchService interface.

SampleSearchServiceImpl - Class in net.sourceforge.seqware.common.business.impl

SampleSearchServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl

SampleService - Interface in net.sourceforge.seqware.common.business

SampleService interface.

SampleServiceImpl - Class in net.sourceforge.seqware.common.business.impl

SampleServiceImpl class.

SampleServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

Constructor for SampleServiceImpl.

SampleSetupController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController

SampleSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleSetupController

Constructor for SampleSetupController.

SampleValidator - Class in net.sourceforge.solexatools.validation

SampleValidator class.

SampleValidator() - Constructor for class net.sourceforge.solexatools.validation.SampleValidator

Constructor for SampleValidator.

SampleWorkflowRunsController - Class in net.sourceforge.solexatools.webapp.controller

SampleWorkflowRunsController class.

SampleWorkflowRunsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController

SanityCheck - Class in io.seqware.pipeline.plugins.sanity

A database validation tool for your SeqWare metadb

SanityCheck() - Constructor for class io.seqware.pipeline.plugins.sanity.SanityCheck

Constructor for HelloWorld.

SanityCheckPluginInterface - Interface in io.seqware.pipeline.plugins.sanity

Specifies an interface for checks that can be done for a SeqWare install

saveAscInSession(HttpServletRequest, String) - Static method in class net.sourceforge.solexatools.util.ControllerUtil

saveAscInSession.

saveAscInSession(HttpServletRequest, String) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

saveAscInSession.

saveFile(MultipartFile, String, Registration) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

saveFile.

saveFile(MultipartFile, String, Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

saveFile.

saveFileForIus(int, int, FileMetadata, int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

saveFileForIus.

saveFileForIus(int, int, FileMetadata, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

saveFileForIus.

saveFileForIus(int, int, FileMetadata, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

saveFileForIus.

saveFileForIus(int, int, FileMetadata, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

saveFileForIus.

SaveOpenNodeController - Class in net.sourceforge.solexatools.webapp.controller

SaveOpenNodeController class.

SaveOpenNodeController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController

Constructor for SaveOpenNodeController.

saveSelectedWorkflowParamValue(HttpServletRequest, Integer, String) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

saveSelectedWorkflowParamValue.

SCHEDULE - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

scheduleInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

scheduleInstalledBundle.

scheduleInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>, String, String, Set<Integer>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

This method just needs a sw_accession value from the workflow table and an ini file(s) in order to schedule a workflow.

scheduleInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine

scheduleInstalledBundle.

scheduleWorkflowRun(int, String, String, String, String, String, String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB

scheduleWorkflowRun.

Script_Check - Class in io.seqware.pipeline.plugins.sanity.checks

Runs through our CLI tutorial

Script_Check() - Constructor for class io.seqware.pipeline.plugins.sanity.checks.Script_Check

scriptFileName(String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob

SCRIPTS_SUBDIR - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

The sub-directory (of the working directory) in which generated script files will be placed.

scriptsDir - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

scriptsDir(String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

SEARCH_CASE_SENSITIVE - Static variable in class net.sourceforge.solexatools.webapp.controller.SearchController

Constant SEARCH_CASE_SENSITIVE="search.checked"

SearchController - Class in net.sourceforge.solexatools.webapp.controller

SearchController class.

SearchController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchController

Constructor for SearchController.

SearchResultsController - Class in net.sourceforge.solexatools.webapp.controller

SearchResultsController class.

SearchResultsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchResultsController

SearchResultsListController - Class in net.sourceforge.solexatools.webapp.controller

SearchResultsListController class.

SearchResultsListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchResultsListController

Constructor for SearchResultsListController.

SecondTierModel - Interface in net.sourceforge.seqware.common.model

This links together all models that do not have sw_accession

secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

Security - Class in net.sourceforge.solexatools

Security class.

Security() - Constructor for class net.sourceforge.solexatools.Security

SELECTED_FILES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

Constant SELECTED_FILES="selectedLaunchFiles"

SELECTED_NODES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

Constant SELECTED_NODES="launchSelectedNodes"

SELECTED_VALUES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

Constant SELECTED_VALUES="selectedWorkflowParamValueId"

selectExperimentNode(List<String>, Study) - Static method in class net.sourceforge.solexatools.util.BulkUtil

selectExperimentNode.

SelectInputController - Class in net.sourceforge.solexatools.webapp.controller

SelectInputController class.

SelectInputController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputController

Constructor for SelectInputController.

SelectInputController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputController

Constructor for SelectInputController.

SelectInputListController - Class in net.sourceforge.solexatools.webapp.controller

SelectInputListController class.

SelectInputListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Constructor for SelectInputListController.

selectIUSNode(List<String>, Sample) - Static method in class net.sourceforge.solexatools.util.BulkUtil

selectIUSNode.

selectProcessingNode(List<String>, WorkflowRun) - Static method in class net.sourceforge.solexatools.util.BulkUtil

selectProcessingNode.

selectProcessingNode(List<String>, Processing) - Static method in class net.sourceforge.solexatools.util.BulkUtil

selectProcessingNode.

selectProcessingNode(List<String>, Lane) - Static method in class net.sourceforge.solexatools.util.BulkUtil

selectProcessingNode.

selectProcessingNode(List<String>, IUS) - Static method in class net.sourceforge.solexatools.util.BulkUtil

selectProcessingNode.

SelectQueryRunner - Class in net.sourceforge.seqware.pipeline.plugins.checkdb

A class that allows plugin writers to only do select queries without any risk of leaving open connections or other unfriendliness

SelectQueryRunner(MetadataDB) - Constructor for class net.sourceforge.seqware.pipeline.plugins.checkdb.SelectQueryRunner

selectSampleNode(List<String>, Experiment) - Static method in class net.sourceforge.solexatools.util.BulkUtil

selectSampleNode.

selectStudyNode(List<String>, List<Study>) - Static method in class net.sourceforge.solexatools.util.BulkUtil

selectStudyNode.

selectWorkflowRunNode(List<String>, List<WorkflowRun>) - Static method in class net.sourceforge.solexatools.util.BulkUtil

selectWorkflowRunNode.

separateFiles(List<ReturnValue>, String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

SEPARATOR - Static variable in class net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController

Constant SEPARATOR="java.io.File.separator"

SEPARATOR - Static variable in class net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController

Constant SEPARATOR="java.io.File.separator"

SEQ_RUN_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant SEQ_RUN_ID="seq_run_id"

SEQUENCER_RUN_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant SEQUENCER_RUN_ATTRIBUTES="Header.SEQUENCER_RUN_ATTRIBUTES.getTitl"{trunked}

SEQUENCER_RUN_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant SEQUENCER_RUN_NAME="Header.SEQUENCER_RUN_NAME.getTitle()"

SEQUENCER_RUN_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant SEQUENCER_RUN_SWA="Header.SEQUENCER_RUN_SWA.getTitle()"

SEQUENCER_RUN_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant SEQUENCER_RUN_TAG_PREFIX="Header.SEQUENCER_RUN_TAG_PREFIX.getTitl"{trunked}

SEQUENCER_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant

Constant SEQUENCER_VIEW="redirect:/sequencerRunList.htm"

SequencerRun - Class in io.seqware.webservice.generated.model

SequencerRun() - Constructor for class io.seqware.webservice.generated.model.SequencerRun

SequencerRun(Integer) - Constructor for class io.seqware.webservice.generated.model.SequencerRun

SequencerRun(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.SequencerRun

SequencerRun - Class in net.sourceforge.seqware.common.model

SequencerRun() - Constructor for class net.sourceforge.seqware.common.model.SequencerRun

Constructor for SequencerRun.

SequencerRunAttribute - Class in io.seqware.webservice.generated.model

SequencerRunAttribute() - Constructor for class io.seqware.webservice.generated.model.SequencerRunAttribute

SequencerRunAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.SequencerRunAttribute

SequencerRunAttribute(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.SequencerRunAttribute

SequencerRunAttribute - Class in net.sourceforge.seqware.common.model

SequencerRunAttribute generated by Morgan Taschuk

SequencerRunAttribute() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute

Constructor for SequencerRunAttribute.

SequencerRunAttribute(int, SequencerRunWizardDTO) - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute

Constructor for SequencerRunAttribute.

SequencerRunAttribute(int, SequencerRunWizardDTO, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute

Constructor for SequencerRunAttribute.

SequencerRunAttributeFacadeREST - Class in io.seqware.webservice.generated.controller

SequencerRunAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SequencerRunAttributeFacadeREST

SequencerRunController - Class in net.sourceforge.solexatools.webapp.controller

SequencerRunController

SequencerRunController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunController

Constructor for SequencerRunController.

SequencerRunController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunController

Constructor for SequencerRunController.

SequencerRunControllerDTO - Class in net.sourceforge.solexatools.webapp.controller

SequencerRunController

SequencerRunControllerDTO() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO

Constructor for SequencerRunControllerDTO.

SequencerRunControllerDTO(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO

Constructor for SequencerRunControllerDTO.

SequencerRunDAO - Interface in net.sourceforge.seqware.common.dao

SequencerRunDAO interface.

SequencerRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

SequencerRunDAOHibernate class.

SequencerRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

Constructor for SequencerRunDAOHibernate.

SequencerRunDTO - Class in net.sourceforge.seqware.common.model

SequencerRunDTO() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunDTO

Constructor for SequencerRunDTO.

SequencerRunFacadeREST - Class in io.seqware.webservice.generated.controller

SequencerRunFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SequencerRunFacadeREST

SequencerRunHtmlUtil - Class in net.sourceforge.solexatools.util

SequencerRunHtmlUtil class.

SequencerRunHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.SequencerRunHtmlUtil

SequencerRunIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries

SequencerRunIdFilesResource class.

SequencerRunIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SequencerRunIdFilesResource

Constructor for SequencerRunIdFilesResource.

SequencerRunIDResource - Class in net.sourceforge.seqware.webservice.resources.tables

SequencerRunIDResource class.

SequencerRunIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource

Constructor for SequencerRunIDResource.

SequencerRunList - Class in net.sourceforge.seqware.common.model.lists

SequencerRunList class.

SequencerRunList() - Constructor for class net.sourceforge.seqware.common.model.lists.SequencerRunList

Constructor for SequencerRunList.

SequencerRunListController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController

SequencerRunListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunListController

Constructor for SequencerRunListController.

SequencerRunListDetailsController - Class in net.sourceforge.solexatools.webapp.controller

SequencerRunListDetailsController class.

SequencerRunListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController

Constructor for SequencerRunListDetailsController.

SequencerRunReport - Class in net.sourceforge.seqware.common.hibernate

SequencerRunReport class.

SequencerRunReport() - Constructor for class net.sourceforge.seqware.common.hibernate.SequencerRunReport

SequencerRunReport.Row - Class in net.sourceforge.seqware.common.hibernate

SequencerRunReport.Row(Date, String, String, String, String, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

SequencerRunReporter - Class in net.sourceforge.seqware.pipeline.plugins

SequencerRunReporter class.

SequencerRunReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter

Constructor for SequencerRunReporter.

SequencerRunReportId - Class in net.sourceforge.seqware.common.model

SequencerRunReportId class.

SequencerRunReportId() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunReportId

SequencerRunReportResource - Class in net.sourceforge.seqware.webservice.resources.queries

SequencerRunReportResource class.

SequencerRunReportResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SequencerRunReportResource

Constructor for SequencerRunReportResource.

SequencerRunReportSetupController - Class in net.sourceforge.solexatools.webapp.controller

SequencerRunReportSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController

SequencerRunReportTableController - Class in net.sourceforge.solexatools.webapp.controller

SequencerRunReportTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

SequencerRunResource - Class in net.sourceforge.seqware.webservice.resources.tables

SequencerRunResource class.

SequencerRunResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource

Constructor for SequencerRunResource.

SequencerRunService - Interface in net.sourceforge.seqware.common.business

SequencerRunService interface.

SequencerRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl

SequencerRunServiceImpl class.

SequencerRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

Constructor for SequencerRunServiceImpl.

SequencerRunSetupController - Class in net.sourceforge.solexatools.webapp.controller

SequencingRunSetupController

SequencerRunSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController

Constructor for SequencerRunSetupController.

SequencerRunSetupControllerDTO - Class in net.sourceforge.solexatools.webapp.controller

SequencingRunSetupController

SequencerRunSetupControllerDTO() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO

Constructor for SequencerRunSetupControllerDTO.

SequencerRunStatus - Enum in net.sourceforge.seqware.common.model

SequencerRunValidator - Class in net.sourceforge.solexatools.validation

SequencerRunValidator class.

SequencerRunValidator() - Constructor for class net.sourceforge.solexatools.validation.SequencerRunValidator

Constructor for SequencerRunValidator.

SequencerRunWizardController - Class in net.sourceforge.solexatools.webapp.controller

SequencerRunWizardController class.

SequencerRunWizardController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Constructor for SequencerRunWizardController.

SequencerRunWizardController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Constructor for SequencerRunWizardController.

SequencerRunWizardDTO - Class in net.sourceforge.seqware.common.model

SequencerRunWizardDTO class.

SequencerRunWizardDTO() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunWizardDTO

Constructor for SequencerRunWizardDTO.

SequencerRunWizardSetupController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp

SequencerRunWizardSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController

Constructor for SequencerRunWizardSetupController.

SequencerRunWizardValidator - Class in net.sourceforge.solexatools.validation

SequencerRunWizardValidator class.

SequencerRunWizardValidator() - Constructor for class net.sourceforge.solexatools.validation.SequencerRunWizardValidator

Constructor for SequencerRunWizardValidator.

SEQWARE_SETTINGS_PROPERTY - Static variable in class net.sourceforge.seqware.common.util.configtools.ConfigTools

Constant SEQWARE_SETTINGS_PROPERTY="SEQWARE_SETTINGS"

SeqwareAccessionIDResource - Class in net.sourceforge.seqware.webservice.resources

SeqwareAccessionIDResource class.

SeqwareAccessionIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource

SeqwareAccessionResource - Class in net.sourceforge.seqware.webservice.resources

SeqwareAccessionResource class.

SeqwareAccessionResource() - Constructor for class net.sourceforge.seqware.webservice.resources.SeqwareAccessionResource

SeqwareException - Exception in net.sourceforge.seqware.common.err

Created by IntelliJ IDEA.

SeqwareException() - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException

Constructor for SeqwareException.

SeqwareException(String) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException

Constructor for SeqwareException.

SeqwareException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException

Constructor for SeqwareException.

SeqwareException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException

Constructor for SeqwareException.

SeqwareExitCode - Class in net.sourceforge.seqware.common.err

Created by IntelliJ IDEA.

SeqwareExitCode() - Constructor for class net.sourceforge.seqware.common.err.SeqwareExitCode

seqwareJar - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

seqwareJarPath - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

seqwareJarPath(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine

SeqWareVerifier - Class in net.sourceforge.seqware.queryengine.webservice.security

SeqWareVerifier class.

SeqWareVerifier() - Constructor for class net.sourceforge.seqware.queryengine.webservice.security.SeqWareVerifier

SeqWareWebServiceApplication - Class in net.sourceforge.seqware.queryengine.webservice.controller

SeqWareWebServiceApplication class.

SeqWareWebServiceApplication() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication

SeqWareWebServiceApplication.OptionalSlashRedirect - Class in net.sourceforge.seqware.queryengine.webservice.controller

http://restlet-discuss.1400322.n2.nabble.com/Proper-handling-of-at-the-end-of-the-requested-URI-td5819896.html

SeqWareWebServiceApplication.OptionalSlashRedirect(Context) - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect

SeqWareWebServiceApplication.OptionalSlashRedirect() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect

SeqWareWebServiceApplicationVersion - Class in net.sourceforge.seqware.queryengine.webservice.controller

SeqWareWebServiceApplicationVersion class.

SeqWareWebServiceApplicationVersion() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion

SeqWareWebServiceApplicationVersion.OptionalSlashRedirect - Class in net.sourceforge.seqware.queryengine.webservice.controller

http://restlet-discuss.1400322.n2.nabble.com/Proper-handling-of-at-the-end-of-the-requested-URI-td5819896.html

SeqWareWebServiceApplicationVersion.OptionalSlashRedirect(Context) - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion.OptionalSlashRedirect

SeqWareWebServiceApplicationVersion.OptionalSlashRedirect() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion.OptionalSlashRedirect

SeqWareWebServiceClient - Class in io.seqware.webservice.client

Separate custom code from base client that would be destroyed during a regeneration

SeqWareWebServiceClient(String) - Constructor for class io.seqware.webservice.client.SeqWareWebServiceClient

Constructor that uses default baseURI

SeqWareWebServiceClient(String, String) - Constructor for class io.seqware.webservice.client.SeqWareWebServiceClient

Constructs a SeqWare web service client for the given resource and url.

SeqWareWebserviceClient - Class in io.seqware.webservice.generated.client

Jersey REST client generated for REST resource:OrganismFacadeREST [io.seqware.webservice.model.organism]
USAGE:

SeqWareWebserviceClient() - Constructor for class io.seqware.webservice.generated.client.SeqWareWebserviceClient

SeqWareWebserviceClient(String) - Constructor for class io.seqware.webservice.generated.client.SeqWareWebserviceClient

Constructs a SeqWare web service client for the given resource and url.

SeqWareWebServiceMain - Class in net.sourceforge.seqware.queryengine.webservice.controller

SeqWareWebServiceMain class.

serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp

serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag

Adag object serialize to element and all its sub objects serialize to sub element

serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn

serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

set_processing_update_tstmp_if_null(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

setAbstract1(String) - Method in class io.seqware.webservice.generated.model.Study

setAbstractStr(String) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field abstractStr.

setAccession(int) - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple

setAccession(int) - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple

setAccession(String) - Method in class io.seqware.webservice.generated.model.Experiment

setAccession(String) - Method in class io.seqware.webservice.generated.model.Organism

setAccession(String) - Method in class io.seqware.webservice.generated.model.Study

setAccession(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field accession.

setAccession(String) - Method in class net.sourceforge.seqware.common.model.Organism

Setter for the field accession.

setAccession(String) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field accession.

setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareExperiment

setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareFile

setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareLane

setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareProcessing

setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareSample

setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareStudy

setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareExperiment

Setter for the field active.

setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareFile

Setter for the field active.

setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareLane

Setter for the field active.

setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareProcessing

Setter for the field active.

setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareSample

Setter for the field active.

setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareStudy

Setter for the field active.

setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

Setter for the field active.

setAdapters(String) - Method in class io.seqware.webservice.generated.model.Sample

setAdapters(String) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field adapters.

setAdapterSpec(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

setAdapterSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Setter for the field adapterSpec.

setAddedSurcharge(BigInteger) - Method in class io.seqware.webservice.generated.model.Expense

setAddedSurcharge(Double) - Method in class net.sourceforge.seqware.common.model.Expense

Setter for the field addedSurcharge.

setAdminModelClass(String) - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple

setAdminModelClass(String) - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple

setAgent(String) - Method in class io.seqware.webservice.generated.model.Expense

setAgent(String) - Method in class net.sourceforge.seqware.common.model.Expense

Setter for the field agent.

setAlgo(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

set the job algorithm

setAlgorithm(String) - Method in class io.seqware.webservice.generated.model.Processing

setAlgorithm(String) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field algorithm.

setAlgorithm(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field algorithm.

setAlgorithm(String) - Method in class net.sourceforge.seqware.pipeline.module.Module

Setter for the field algorithm.

setAlias(String) - Method in class io.seqware.webservice.generated.model.Experiment

setAlias(String) - Method in class io.seqware.webservice.generated.model.Ius

setAlias(String) - Method in class io.seqware.webservice.generated.model.Lane

setAlias(String) - Method in class io.seqware.webservice.generated.model.Sample

setAlias(String) - Method in class io.seqware.webservice.generated.model.Study

setAlias(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field alias.

setAlias(String) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field alias.

setAlias(String) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field alias.

setAlias(String) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field alias.

setAlign(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel

setAllInputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Setter for the field allInputFiles.

setAllItems(String) - Method in class net.sourceforge.solexatools.util.PageInfo

Setter for the field allItems.

setAncestorWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.Processing

setAnonymizedName(String) - Method in class io.seqware.webservice.generated.model.Sample

setAnonymizedName(String) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field anonymizedName.

setArch(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

setArgs(String[]) - Method in class net.sourceforge.seqware.pipeline.tools.ReportTest.TestThread

setArguments(List<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command

setAssayType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of assayType

setAsText(String) - Method in class net.sourceforge.solexatools.validation.CustomIntegerEditor

setAttached(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

setAttribute(String, String) - Method in class net.sourceforge.seqware.common.module.ReturnValue

setAttribute.

setAttributeParent(T) - Method in interface net.sourceforge.seqware.common.model.Attribute

Associate this attribute with its parent

setAttributeParent(Experiment) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

setAttributeParent(File) - Method in class net.sourceforge.seqware.common.model.FileAttribute

setAttributeParent(IUS) - Method in class net.sourceforge.seqware.common.model.IUSAttribute

setAttributeParent(Lane) - Method in class net.sourceforge.seqware.common.model.LaneAttribute

setAttributeParent(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

setAttributeParent(Sample) - Method in class net.sourceforge.seqware.common.model.SampleAttribute

setAttributeParent(SampleSearch) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute

setAttributeParent(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

setAttributeParent(Study) - Method in class net.sourceforge.seqware.common.model.StudyAttribute

setAttributeParent(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute

setAttributeParent(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute

setAttributes(Map<String, String>) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field attributes.

setAttributes(Set<AttributeDto>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Setter for the field attributes.

setAttributes(Set<AttributeDto>) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto

Setter for the field attributes.

setBarcode(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Set the value of barcode

setBarcode(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Setter for the field barcode.

setBaseCaller(String) - Method in class io.seqware.webservice.generated.model.Experiment

setBaseCaller(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setBaseCaller(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field baseCaller.

setBaseCoord(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

setBaseCoord(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Setter for the field baseCoord.

setBaseDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field baseDir.

setBaseIniFile(String) - Method in class io.seqware.webservice.generated.model.Workflow

setBaseIniFile(String) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field baseIniFile.

setCell(List<String>) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells

setCenterName(String) - Method in class io.seqware.webservice.generated.model.Experiment

setCenterName(String) - Method in class io.seqware.webservice.generated.model.Study

setCenterName(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field centerName.

setCenterName(String) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field centerName.

setCenterProjectName(String) - Method in class io.seqware.webservice.generated.model.Study

setCenterProjectName(String) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field centerProjectName.

setChildId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingRelationship

setChildId(Sample) - Method in class io.seqware.webservice.generated.model.SampleRelationship

setChildren(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field children.

setChildren(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field children.

setChildrenUrls(Set<String>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Setter for the field childrenUrls.

setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.FileReportRow

Setter for the field childSample.

setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Setter for the field childSample.

setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId

Setter for the field childSample.

setChildSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Setter for the field childSample.

setChildSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Setter for the field childSample.

setChildSampleId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport

setChildSampleId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport

setClassesDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field classesDir.

setClient(Client) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

setClientNotes(String) - Method in class io.seqware.webservice.generated.model.Invoice

setClientNotes(String) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field clientNotes.

setCmd(String) - Method in class io.seqware.webservice.generated.model.Workflow

setCmd(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setCode(String) - Method in class io.seqware.webservice.generated.model.LaneType

setCode(String) - Method in class io.seqware.webservice.generated.model.Organism

setCode(String) - Method in class net.sourceforge.seqware.common.model.Organism

Setter for the field code.

setCode(String) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto

Setter for the field code.

setColorMatrix(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setColorMatrix(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field colorMatrix.

setColorMatrix(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field colorMatrix.

setColorMatrixCode(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setColorMatrixCode(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field colorMatrixCode.

setColorMatrixCode(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field colorMatrixCode.

setCommand(String) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field command.

setCommand(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field command.

setCommand(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field command.

setCommand(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

setCommand(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

set the job command

setCommand(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

setCommonName(String) - Method in class io.seqware.webservice.generated.model.Sample

setCompleted(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Setter for the field completed.

setCompute(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setComputeReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field computeReq.

setConfig(Map<String, String>) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface

Let's you set the config this object should use.

setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin

Let's you set the config this object should use.

setConfig(Map<String, String>) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface

Let's you set the config this object should use.

setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld

Let's you set the config this object should use.

setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin

Let's you set the config this object should use.

setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin

Let's you set the config this object should use.

setConfigPath(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field configPath.

setConfigs(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

set the key-value properties for workflow

setConfirmEmailAddress(String) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO

Setter for the field confirmEmailAddress.

setConfirmPassword(String) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO

Setter for the field confirmPassword.

setConstructionProtocol(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

setConstructionProtocol(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Setter for the field constructionProtocol.

setCountFile(Integer) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field countFile.

setCreated(Date) - Method in class net.sourceforge.seqware.common.model.SampleSearch

Setter for the field created.

setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field createTimestamp.

setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field createTimestamp.

setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field createTimestamp.

setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field createTimestamp.

setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field createTimestamp.

setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Registration

Setter for the field createTimestamp.

setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field createTimestamp.

setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field createTimestamp.

setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field createTimestamp.

setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareStudy

Setter for the field createTimestamp.

setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

Setter for the field createTimestamp.

setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field createTimestamp.

setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field createTimestamp.

setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field createTimestamp.

setCreateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Setter for the field createTimeStamp.

setCreateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Setter for the field createTimeStamp.

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Experiment

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Invoice

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Ius

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Lane

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Processing

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Registration

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Sample

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.SampleSearch

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.SequencerRun

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareExperiment

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareFile

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareLane

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareProcessing

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareSample

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareStudy

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Study

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Workflow

setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareExperiment

Setter for the field createTstmp.

setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareFile

Setter for the field createTstmp.

setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareLane

Setter for the field createTstmp.

setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareProcessing

Setter for the field createTstmp.

setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareSample

Setter for the field createTstmp.

setCriteria(String) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController

Setter for the field criteria.

setCurrentSelectedFiles(HttpServletRequest, List<File>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

setCurrentSelectedFiles.

setCurrentSelectedNodes(HttpServletRequest, List<String>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil

setCurrentSelectedNodes.

setCurrentWorkingDir(String) - Method in class io.seqware.webservice.generated.model.Workflow

setCurrentWorkingDir(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setCurrentWorkingDir(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field currentWorkingDir.

setCwd(String) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field cwd.

setCycleCoord(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

setCycleCoord(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Setter for the field cycleCoord.

setCycleCount(Integer) - Method in class io.seqware.webservice.generated.model.Lane

setCycleCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun

setCycleCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field cycleCount.

setCycleCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field cycleCount.

setCycleDescriptor(String) - Method in class io.seqware.webservice.generated.model.Lane

setCycleDescriptor(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field cycleDescriptor.

setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field cycleDescriptor.

setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field cycleDescriptor.

setCycles(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field cycles.

setCycles(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field cycles.

setCycleSequence(String) - Method in class io.seqware.webservice.generated.model.Lane

setCycleSequence(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setCycleSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field cycleSequence.

setCycleSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field cycleSequence.

setDataDecryptionKeyString(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Sets data decryption key.

setDataEncryptionKeyString(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Sets data encryption key.

setDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

setDate(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

set the pre-defined date variable

setDax(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setDax(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field dax.

setDaxDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setDaysUntilDue(Integer) - Method in class io.seqware.webservice.generated.model.Invoice

setDaysUntilDue(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field daysUntilDue.

setDb(String) - Method in class io.seqware.webservice.generated.model.ExperimentLink

setDb(String) - Method in class io.seqware.webservice.generated.model.IusLink

setDb(String) - Method in class io.seqware.webservice.generated.model.LaneLink

setDb(String) - Method in class io.seqware.webservice.generated.model.SampleLink

setDb(String) - Method in class io.seqware.webservice.generated.model.StudyLink

setDb(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink

Setter for the field db.

setDb(String) - Method in class net.sourceforge.seqware.common.model.IUSLink

Setter for the field db.

setDb(String) - Method in class net.sourceforge.seqware.common.model.LaneLink

Setter for the field db.

setDb(String) - Method in class net.sourceforge.seqware.common.model.SampleLink

Setter for the field db.

setDb(String) - Method in class net.sourceforge.seqware.common.model.StudyLink

Setter for the field db.

setDecodeMethod(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

setDecodeMethod(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Setter for the field decodeMethod.

setDefaultValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam

setDefaultValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Setter for the field defaultValue.

setDescription(String) - Method in class io.seqware.webservice.generated.model.Expense

setDescription(String) - Method in class io.seqware.webservice.generated.model.Experiment

setDescription(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

setDescription(String) - Method in class io.seqware.webservice.generated.model.File

setDescription(String) - Method in class io.seqware.webservice.generated.model.Ius

setDescription(String) - Method in class io.seqware.webservice.generated.model.Lane

setDescription(String) - Method in class io.seqware.webservice.generated.model.LibrarySelection

setDescription(String) - Method in class io.seqware.webservice.generated.model.LibrarySource

setDescription(String) - Method in class io.seqware.webservice.generated.model.LibraryStrategy

setDescription(String) - Method in class io.seqware.webservice.generated.model.Platform

setDescription(String) - Method in class io.seqware.webservice.generated.model.Processing

setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingIus

setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingLanes

setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingSamples

setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingStudies

setDescription(String) - Method in class io.seqware.webservice.generated.model.Sample

setDescription(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setDescription(String) - Method in class io.seqware.webservice.generated.model.Study

setDescription(String) - Method in class io.seqware.webservice.generated.model.StudyType

setDescription(String) - Method in class io.seqware.webservice.generated.model.Workflow

setDescription(String) - Method in class net.sourceforge.seqware.common.model.Expense

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibrarySelection

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibrarySource

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.Platform

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.StudyType

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata

setDescription(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto

Setter for the field description.

setDescription(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Setter for the field description.

setDeveloperMl(boolean) - Method in class io.seqware.webservice.generated.model.Registration

setDisplay(Boolean) - Method in class io.seqware.webservice.generated.model.WorkflowParam

setDisplay(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Setter for the field display.

setDisplay(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel

setDisplayName(String) - Method in class io.seqware.webservice.generated.model.FileType

setDisplayName(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam

setDisplayName(String) - Method in class io.seqware.webservice.generated.model.WorkflowParamValue

setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.FileType

Setter for the field displayName.

setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Setter for the field displayName.

setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

Setter for the field displayName.

setDisplayName(String) - Method in class net.sourceforge.solexatools.util.SummaryLine

Setter for the field displayName.

setDisplayValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Setter for the field displayValue.

setDomainObject(Registration) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO

Setter for the field domainObject.

setDomainObject(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO

Setter for the field domainObject.

setEarliestDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport

Set the value of earliestDate.

setEmail(String) - Method in class io.seqware.webservice.generated.model.Registration

setEmail(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto

Setter for the field email.

setEmailAddress(String) - Method in class net.sourceforge.seqware.common.model.Registration

Setter for the field emailAddress.

setEnd(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field end.

setEndDate(Date) - Method in class io.seqware.webservice.generated.model.Invoice

setEndDate(Date) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field endDate.

setEndPage(String) - Method in class net.sourceforge.solexatools.util.PageInfo

Setter for the field endPage.

setEntityUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto

Setter for the field entityUrl.

setErrorCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field errorCount.

setExecutionEnv(Environment.ExecutionEnvironment) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

set the execution environment

setExistingType(StudyType) - Method in class io.seqware.webservice.generated.model.Study

setExistingType(StudyType) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field existingType.

setExistingTypeInt(Integer) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field existingTypeInt.

setExitCode(int) - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException

Setter for the field exitCode.

setExitStatus(Integer) - Method in class io.seqware.webservice.generated.model.Processing

setExitStatus(Integer) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field exitStatus.

setExitStatus(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field exitStatus.

setExpectedBasecall(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

setExpectedBaseCall(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Setter for the field expectedBaseCall.

setExpectedNumberReads(BigInteger) - Method in class io.seqware.webservice.generated.model.Experiment

setExpectedNumberReads(Integer) - Method in class io.seqware.webservice.generated.model.Sample

setExpectedNumberReads(Long) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field expectedNumberReads.

setExpectedNumberRuns(Integer) - Method in class io.seqware.webservice.generated.model.Experiment

setExpectedNumberRuns(Integer) - Method in class io.seqware.webservice.generated.model.Sample

setExpectedNumberRuns(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field expectedNumberRuns.

setExpectedNumberSpots(BigInteger) - Method in class io.seqware.webservice.generated.model.Experiment

setExpectedNumberSpots(Integer) - Method in class io.seqware.webservice.generated.model.Sample

setExpectedNumberSpots(Long) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field expectedNumberSpots.

setExpectedNumReads(Integer) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field expectedNumReads.

setExpectedNumRuns(Integer) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field expectedNumRuns.

setExpectedNumSpots(Integer) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field expectedNumSpots.

setExpenseAttributeCollection(Collection<ExpenseAttribute>) - Method in class io.seqware.webservice.generated.model.Expense

setExpenseAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute

setExpenseCollection(Collection<Expense>) - Method in class io.seqware.webservice.generated.model.Invoice

setExpenseFinishedTstmp(Date) - Method in class io.seqware.webservice.generated.model.Expense

setExpenseId(Integer) - Method in class io.seqware.webservice.generated.model.Expense

setExpenseId(Expense) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute

setExpenseId(Integer) - Method in class net.sourceforge.seqware.common.model.Expense

Setter for the field expenseId.

setExpenses(Set<Expense>) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field expenses.

setExpenseType(String) - Method in class io.seqware.webservice.generated.model.Expense

setExpenseType(String) - Method in class net.sourceforge.seqware.common.model.Expense

Setter for the field expenseType.

setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

Setter for the field experiment.

setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ExperimentLink

Setter for the field experiment.

setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.FileReportRow

Setter for the field experiment.

setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments

Setter for the field experiment.

setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field experiment.

setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ShareExperiment

Setter for the field experiment.

setExperiment(Experiment, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setExperiment.

setExperimentAttributeCollection(Collection<ExperimentAttribute>) - Method in class io.seqware.webservice.generated.model.Experiment

setExperimentAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute

setExperimentAttributeId(int) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

Setter for the field experimentAttributeId.

setExperimentAttributes(Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field experimentAttributes.

setExperimentAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of experimentAttributes

setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.Platform

setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.Registration

setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.Study

setExperimentDAO(ExperimentDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

setExperimentDAO.

setExperimentDAO(ExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

setExperimentDAO.

setExperimentDAO(ExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

Setter for the field experimentDAO.

setExperimentDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of experimentDescription

setExperimentId(Integer) - Method in class io.seqware.webservice.generated.model.Experiment

setExperimentId(Experiment) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute

setExperimentId(Experiment) - Method in class io.seqware.webservice.generated.model.ExperimentLink

setExperimentId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport

setExperimentId(Experiment) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

setExperimentId(Experiment) - Method in class io.seqware.webservice.generated.model.Sample

setExperimentId(Experiment) - Method in class io.seqware.webservice.generated.model.ShareExperiment

setExperimentId(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field experimentId.

setExperimentLibraryDesign(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field experimentLibraryDesign.

setExperimentLibraryDesignCollection(Collection<ExperimentLibraryDesign>) - Method in class io.seqware.webservice.generated.model.LibrarySelection

setExperimentLibraryDesignCollection(Collection<ExperimentLibraryDesign>) - Method in class io.seqware.webservice.generated.model.LibrarySource

setExperimentLibraryDesignCollection(Collection<ExperimentLibraryDesign>) - Method in class io.seqware.webservice.generated.model.LibraryStrategy

setExperimentLibraryDesignDAO(ExperimentLibraryDesignDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService

setExperimentLibraryDesignDAO.

setExperimentLibraryDesignDAO(ExperimentLibraryDesignDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl

setExperimentLibraryDesignDAO.

setExperimentLibraryDesignId(ExperimentLibraryDesign) - Method in class io.seqware.webservice.generated.model.Experiment

setExperimentLibraryDesignId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

setExperimentLibraryDesignId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Setter for the field experimentLibraryDesignId.

setExperimentLibraryDesignService(ExperimentLibraryDesignService) - Method in class net.sourceforge.seqware.common.ContextImpl

setExperimentLibraryDesignService(ExperimentLibraryDesignService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Setter for the field experimentLibraryDesignService.

setExperimentLinkCollection(Collection<ExperimentLink>) - Method in class io.seqware.webservice.generated.model.Experiment

setExperimentLinkId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentLink

setExperimentLinkId(int) - Method in class net.sourceforge.seqware.common.model.ExperimentLink

Setter for the field experimentLinkId.

setExperimentLinks(Set<ExperimentLink>) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field experimentLinks.

setExperimentName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of experimentName

setExperiments(Set<Experiment>) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field experiments.

setExperiments(SortedSet<Experiment>) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field experiments.

setExperimentService(ExperimentService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Setter for the field experimentService.

setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Setter for the field experimentService.

setExperimentSpotDesign(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field experimentSpotDesign.

setExperimentSpotDesign(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Setter for the field experimentSpotDesign.

setExperimentSpotDesignDAO(ExperimentSpotDesignDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService

setExperimentSpotDesignDAO.

setExperimentSpotDesignDAO(ExperimentSpotDesignDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl

setExperimentSpotDesignDAO.

setExperimentSpotDesignId(ExperimentSpotDesign) - Method in class io.seqware.webservice.generated.model.Experiment

setExperimentSpotDesignId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

setExperimentSpotDesignId(ExperimentSpotDesign) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

setExperimentSpotDesignId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Setter for the field experimentSpotDesignId.

setExperimentSpotDesignReadSpecCollection(Collection<ExperimentSpotDesignReadSpec>) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

setExperimentSpotDesignReadSpecDAO(ExperimentSpotDesignReadSpecDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService

setExperimentSpotDesignReadSpecDAO.

setExperimentSpotDesignReadSpecDAO(ExperimentSpotDesignReadSpecDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl

setExperimentSpotDesignReadSpecDAO.

setExperimentSpotDesignReadSpecId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

setExperimentSpotDesignReadSpecId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Setter for the field experimentSpotDesignReadSpecId.

setExperimentSpotDesignReadSpecService(ExperimentSpotDesignReadSpecService) - Method in class net.sourceforge.seqware.common.ContextImpl

setExperimentSpotDesignReadSpecService(ExperimentSpotDesignReadSpecService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Setter for the field experimentSpotDesignReadSpecService.

setExperimentSpotDesignService(ExperimentSpotDesignService) - Method in class net.sourceforge.seqware.common.ContextImpl

setExperimentSpotDesignService(ExperimentSpotDesignService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Setter for the field experimentSpotDesignService.

setExperimentSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

setExpLibDesignDesc(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field expLibDesignDesc.

setExpLibDesignName(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field expLibDesignName.

setExpLibDesignProtocol(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field expLibDesignProtocol.

setExpLibDesignSelection(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field expLibDesignSelection.

setExpLibDesignSource(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field expLibDesignSource.

setExpLibDesignStrategy(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field expLibDesignStrategy.

setExpSpotDesignAdapterSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field expSpotDesignAdapterSpec.

setExpSpotDesignReadsPerSpot(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field expSpotDesignReadsPerSpot.

setExpSpotDesignTagSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field expSpotDesignTagSpec.

setExtension(String) - Method in class io.seqware.webservice.generated.model.FileType

setExtension(String) - Method in class net.sourceforge.seqware.common.model.FileType

Setter for the field extension.

setExternalId(String) - Method in class io.seqware.webservice.generated.model.Invoice

setExternalId(String) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field externalId.

setFailed(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Setter for the field failed.

setFile(MultipartFile) - Method in class net.sourceforge.seqware.common.business.UploadFile

Setter for the field file.

setFile(File) - Method in class net.sourceforge.seqware.common.model.FileAttribute

Setter for the field file.

setFile(File) - Method in class net.sourceforge.seqware.common.model.FileReportRow

Setter for the field file.

setFile(File) - Method in class net.sourceforge.seqware.common.model.ShareFile

Setter for the field file.

setFile(File) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Setter for the field file.

setFileAttributeCollection(Collection<FileAttribute>) - Method in class io.seqware.webservice.generated.model.File

setFileAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.FileAttribute

setFileAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.FileAttribute

Setter for the field fileAttributeId.

setFileAttributes(Set<FileAttribute>) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field fileAttributes.

setFileCollection(Collection<File>) - Method in class io.seqware.webservice.generated.model.FileType

setFileCollection(Collection<File>) - Method in class io.seqware.webservice.generated.model.Registration

setFileCollection(Collection<File>) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setFileDAO(FileDAO) - Method in interface net.sourceforge.seqware.common.business.FileService

setFileDAO.

setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

Sets a private member variable with an instance of an implementation of FileDAO.

setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

setFileDAO.

setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

Sets a private member variable with an instance of an implementation of FileDAO.

setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

Setter for the field fileDAO.

setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

Sets a private member variable with an instance of an implementation of FileDAO.

setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

Sets a private member variable with an instance of an implementation of FileDAO.

setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

Sets a private member variable with an instance of an implementation of FileDAO.

setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

Sets a private member variable with an instance of an implementation of FileDAO.

setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

Sets a private member variable with an instance of an implementation of FileDAO.

setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

Sets a private member variable with an instance of an implementation of FileDAO.

setFileForSequrncerRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setFileForSequrncerRun.

setFileForStudy(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setFileForStudy.

setFileForWorkflowRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setFileForWorkflowRun.

setFileForWorkflowRunRunning(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setFileForWorkflowRunRunning.

setFileId(Integer) - Method in class io.seqware.webservice.generated.model.File

setFileId(File) - Method in class io.seqware.webservice.generated.model.FileAttribute

setFileId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport

setFileId(File) - Method in class io.seqware.webservice.generated.model.ProcessingFiles

setFileId(File) - Method in class io.seqware.webservice.generated.model.ShareFile

setFileId(Integer) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field fileId.

setFileMetaType(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam

setFileMetaType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Setter for the field fileMetaType.

setFileMetaType(String) - Method in class net.sourceforge.solexatools.util.SummaryLine

Setter for the field fileMetaType.

setFilename(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

setFilename(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

setFileOne(MultipartFile) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field fileOne.

setFilePath(String) - Method in class io.seqware.webservice.generated.model.File

setFilePath(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setFilePath(String) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field filePath.

setFilePath(String) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field filePath.

setFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field filePath.

setFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field filePath.

setFilePath(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata

setFilePath(File) - Method in class net.sourceforge.seqware.common.module.FileMetadata

setFilePath(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto

Setter for the field filePath.

setFileReportDAO(FileReportDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl

Setter for the field fileReportDAO.

setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Setter for the field fileReportService.

setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController

Setter for the field fileReportService.

setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Setter for the field fileReportService.

setFiles(Set<File>) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field files.

setFiles(List<File>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Setter for the field files.

setFiles(ArrayList<FileMetadata>) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field files.

setFiles(List<File>) - Method in class net.sourceforge.solexatools.util.SummaryLine

Setter for the field files.

setFiles_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Setter for the field files_url.

setFilesArray(ArrayList<File>) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

Setter for the field filesArray.

setFileService(FileService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.FileController

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Setter for the field fileService.

setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Setter for the field fileService.

setFileStatus(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

setFileSwa(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

setFileTwo(MultipartFile) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field fileTwo.

setFileTwoURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field fileTwoURL.

setFileType(FileType) - Method in class net.sourceforge.seqware.common.business.UploadFile

Setter for the field fileType.

setFileType(FileType) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field fileType.

setFileType(FileType) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field fileType.

setFileTypeDAO(FileTypeDAO) - Method in interface net.sourceforge.seqware.common.business.FileTypeService

setFileTypeDAO.

setFileTypeDAO(FileTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl

setFileTypeDAO.

setFileTypeDAO(FileTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

Setter for the field fileTypeDAO.

setFileTypeId(FileType) - Method in class io.seqware.webservice.generated.model.File

setFileTypeId(Integer) - Method in class io.seqware.webservice.generated.model.FileType

setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.business.UploadFile

Setter for the field fileTypeId.

setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.FileType

Setter for the field fileTypeId.

setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field fileTypeId.

setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator

Setter for the field fileTypeService.

setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator

Setter for the field fileTypeService.

setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Setter for the field fileTypeService.

setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Setter for the field fileTypeService.

setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Setter for the field fileTypeService.

setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController

Setter for the field fileTypeService.

setFileUploadService(FileUploadService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Setter for the field fileUploadService.

setFileURL(String) - Method in class net.sourceforge.seqware.common.business.UploadFile

Setter for the field fileURL.

setFileURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field fileURL.

setFinalized(Boolean) - Method in class io.seqware.webservice.generated.model.Invoice

setFinalized(boolean) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field finalized.

setFinishedTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Expense

Setter for the field finishedTimestamp.

setFirstName(String) - Method in class io.seqware.webservice.generated.model.Registration

setFirstName(String) - Method in class net.sourceforge.seqware.common.model.Registration

Setter for the field firstName.

setFirstName(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto

Setter for the field firstName.

setFlowCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun

setFlowCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field flowCount.

setFlowCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field flowCount.

setFlowSequence(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setFlowSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field flowSequence.

setFlowSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field flowSequence.

setFolderStore(String) - Method in class net.sourceforge.seqware.common.business.UploadFile

Setter for the field folderStore.

setFolderStore(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field folderStore.

setForceCopy(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

when forceCopy is true, it will pass "--forcecopy" argument to provisionFileJob

setForceRunAll(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

setFs_default_name(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setFs_defaultFS(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setFs_hdfs_impl(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setFullyPaid(Boolean) - Method in class io.seqware.webservice.generated.model.Invoice

setFullyPaid(boolean) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field fullyPaid.

setGcrOutputFile(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command

setGcrSkipIfMissing(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command

setGcrSkipIfOutputExists(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command

setGroupingStrategy(FindAllTheFiles.Header) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

setHasMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

setHasMetadataWriteback(boolean) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

job specific metadata is not supported yet

setHasMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

setHbase_master(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setHbase_zookeeper_property_clientPort(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setHbase_zookeeper_quorum(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setHeader(FindAllTheFiles.Header) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

Deprecated.

setHost(String) - Method in class io.seqware.webservice.generated.model.Workflow

setHost(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setHost(String) - Method in class net.sourceforge.seqware.common.model.Workflow

Deprecated.

setHost(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field host.

setHost(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field host.

setHtml(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field html.

setHtml(String) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field html.

setHtml(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field html.

setId(int) - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple

setId(int) - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple

setId(String) - Method in class io.seqware.webservice.generated.model.ExperimentLink

setId(String) - Method in class io.seqware.webservice.generated.model.IusLink

setId(String) - Method in class io.seqware.webservice.generated.model.LaneLink

setId(String) - Method in class io.seqware.webservice.generated.model.SampleLink

setId(String) - Method in class io.seqware.webservice.generated.model.StudyLink

setId(Integer) - Method in class net.sourceforge.seqware.common.business.UploadFile

Setter for the field id.

setId(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink

Setter for the field id.

setId(String) - Method in class net.sourceforge.seqware.common.model.IUSLink

Setter for the field id.

setId(String) - Method in class net.sourceforge.seqware.common.model.LaneLink

Setter for the field id.

setId(String) - Method in class net.sourceforge.seqware.common.model.SampleLink

Setter for the field id.

setId(String) - Method in class net.sourceforge.seqware.common.model.StudyLink

Setter for the field id.

setId(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

set the job id

setIdentitySamples(Collection<Sample>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Setter for the field identitySamples.

setImmediateInputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Setter for the field immediateInputFiles.

setIndividualName(String) - Method in class io.seqware.webservice.generated.model.Sample

setIndividualName(String) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field individualName.

setIndividualNumber(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

setInfo(String) - Method in class net.sourceforge.solexatools.util.PageInfo

Setter for the field info.

setIniFile(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setIniFile(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field iniFile.

setInputAlgorithm(String) - Method in class io.seqware.webservice.generated.model.Workflow

setInputAlgorithm(String) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field inputAlgorithm.

setInputFileAccessions(Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

setInstalled(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

setInstitution(String) - Method in class io.seqware.webservice.generated.model.Registration

setInstitution(String) - Method in class net.sourceforge.seqware.common.model.Registration

Setter for the field institution.

setInstitution(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto

Setter for the field institution.

setInstrumentModel(String) - Method in class io.seqware.webservice.generated.model.Platform

setInstrumentModel(String) - Method in class net.sourceforge.seqware.common.model.Platform

Setter for the field instrumentModel.

setInstrumentName(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setInstrumentName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field instrumentName.

setInstrumentName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field instrumentName.

setInvitationCode(String) - Method in class io.seqware.webservice.generated.model.Registration

setInvitationCode(String) - Method in class net.sourceforge.seqware.common.model.Registration

Setter for the field invitationCode.

setInvoice(Invoice) - Method in class net.sourceforge.seqware.common.model.Expense

Setter for the field invoice.

setInvoiceAttributeCollection(Collection<InvoiceAttribute>) - Method in class io.seqware.webservice.generated.model.Invoice

setInvoiceAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute

setInvoiceCollection(Collection<Invoice>) - Method in class io.seqware.webservice.generated.model.Registration

setInvoiceDAO(InvoiceDAO) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl

setInvoiceDAO.

setInvoiceDAO(InvoiceDAO) - Method in interface net.sourceforge.seqware.common.business.InvoiceService

setInvoiceDAO.

setInvoiceId(Invoice) - Method in class io.seqware.webservice.generated.model.Expense

setInvoiceId(Integer) - Method in class io.seqware.webservice.generated.model.Invoice

setInvoiceId(Invoice) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute

setInvoiceId(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field invoiceId.

setInvoiceService(InvoiceService) - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController

Setter for the field invoiceService.

setInvoiceService(InvoiceService) - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController

Setter for the field invoiceService.

setIsEnd(boolean) - Method in class net.sourceforge.solexatools.util.PageInfo

Setter for the field isEnd.

setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field isHasFile.

setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field isHasFile.

setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field isHasFile.

setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field isHasFile.

setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field isHasFile.

setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field isHasFile.

setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field isHasFile.

setIsInput(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

isInput = @param isInput isOutput = !@param isInput

setIsOutput(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

isInput = !@param isOutput isOutput = @param isOutput

setIsPublic(Boolean) - Method in class io.seqware.webservice.generated.model.Sample

setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field isSelected.

setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field isSelected.

setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field isSelected.

setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field isSelected.

setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field isSelected.

setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field isSelected.

setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field isSelected.

setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field isSelected.

setIsStart(boolean) - Method in class net.sourceforge.solexatools.util.PageInfo

Setter for the field isStart.

setIus(IUS) - Method in class net.sourceforge.seqware.common.model.FileReportRow

Setter for the field ius.

setIus(IUS) - Method in class net.sourceforge.seqware.common.model.IUSAttribute

Setter for the field ius.

setIus(IUS) - Method in class net.sourceforge.seqware.common.model.IUSLink

Setter for the field ius.

setIUS(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.Lane

setIUS.

setIUS(Set<IUS>) - Method in class net.sourceforge.seqware.common.model.Processing

setIUS.

setIus(IUS) - Method in class net.sourceforge.seqware.common.model.ProcessingIus

Setter for the field ius.

setIUS(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.Sample

setIUS.

setIus(IUS) - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Setter for the field ius.

setIus(IUS) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId

Setter for the field ius.

setIus(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field ius.

setIus(IUS) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Setter for the field ius.

setIusAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Adds a new ius attribute if the tag does not exist for this ius, or changes the value of an existing ius attribute.

setIusAttributeCollection(Collection<IusAttribute>) - Method in class io.seqware.webservice.generated.model.Ius

setIusAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.IusAttribute

setIusAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.IUSAttribute

Setter for the field iusAttributeId.

setIusAttributes(Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field iusAttributes.

setIusAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Set the value of iusAttributes

setIusCollection(Collection<Ius>) - Method in class io.seqware.webservice.generated.model.Lane

setIusCollection(Collection<Ius>) - Method in class io.seqware.webservice.generated.model.Registration

setIusCollection(Collection<Ius>) - Method in class io.seqware.webservice.generated.model.Sample

setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

setIUSDAO.

setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

setIUSDAO.

setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

Sets a private member variable with an instance of an implementation of IUSDAO.

setIUSDAO(IUSDAO) - Method in interface net.sourceforge.seqware.common.business.IUSService

setIUSDAO.

setIusDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Set the value of iusDescription

setIusId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport

setIusId(Integer) - Method in class io.seqware.webservice.generated.model.Ius

setIusId(Ius) - Method in class io.seqware.webservice.generated.model.IusAttribute

setIusId(Ius) - Method in class io.seqware.webservice.generated.model.IusLink

setIusId(Ius) - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns

setIusId(Ius) - Method in class io.seqware.webservice.generated.model.ProcessingIus

setIusId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport

setIusId(Integer) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field iusId.

setIusLinkCollection(Collection<IusLink>) - Method in class io.seqware.webservice.generated.model.Ius

setIusLinkId(Integer) - Method in class io.seqware.webservice.generated.model.IusLink

setIusLinkId(int) - Method in class net.sourceforge.seqware.common.model.IUSLink

Setter for the field iusLinkId.

setIusLinks(Set<IUSLink>) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field iusLinks.

setIusName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Set the value of iusName

setIusService(IUSService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field iusService.

setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Setter for the field iusService.

setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

setIUSService.

setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController

setIUSService.

setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController

Setter for the field iusService.

setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController

setIUSService.

setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController

Setter for the field iusService.

setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController

Setter for the field iusService.

setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController

setIUSService.

setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Setter for the field iusService.

setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

setIUSService.

setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController

setIUSService.

setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Setter for the field iusService.

setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

setIUSService.

setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController

Setter for the field iusService.

setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController

setIUSService.

setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

Setter for the field iusService.

setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

setIUSService.

setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

setIUSService.

setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Setter for the field iusService.

setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

setIUSService.

setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Setter for the field iusService.

setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

setIUSService.

setIusSkip(boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Set the value of iusSkip

setIusSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

setIusWorkflowRunsCollection(Collection<IusWorkflowRuns>) - Method in class io.seqware.webservice.generated.model.Ius

setIusWorkflowRunsCollection(Collection<IusWorkflowRuns>) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setIusWorkflowRunsId(Integer) - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns

setJoinDevelopersMailingList(boolean) - Method in class net.sourceforge.seqware.common.model.Registration

Setter for the field joinDevelopersMailingList.

setJoinUsersMailingList(boolean) - Method in class net.sourceforge.seqware.common.model.Registration

Setter for the field joinUsersMailingList.

setKey(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam

setKey(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

setKey(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Setter for the field key.

setKey(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

Setter for the field key.

setKey(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument

Setter for the field key.

setKey(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile

Setter for the field key.

setLabel(String) - Method in class io.seqware.webservice.generated.model.ExperimentLink

setLabel(String) - Method in class io.seqware.webservice.generated.model.IusLink

setLabel(String) - Method in class io.seqware.webservice.generated.model.LaneLink

setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingIus

setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingLanes

setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingSamples

setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingStudies

setLabel(String) - Method in class io.seqware.webservice.generated.model.SampleLink

setLabel(String) - Method in class io.seqware.webservice.generated.model.StudyLink

setLabel(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink

Setter for the field label.

setLabel(String) - Method in class net.sourceforge.seqware.common.model.IUSLink

Setter for the field label.

setLabel(String) - Method in class net.sourceforge.seqware.common.model.LaneLink

Setter for the field label.

setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments

Setter for the field label.

setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus

Setter for the field label.

setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes

Setter for the field label.

setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples

Setter for the field label.

setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Setter for the field label.

setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies

Setter for the field label.

setLabel(String) - Method in class net.sourceforge.seqware.common.model.SampleLink

Setter for the field label.

setLabel(String) - Method in class net.sourceforge.seqware.common.model.StudyLink

Setter for the field label.

setLane(Lane) - Method in class net.sourceforge.seqware.common.model.FileReportRow

Setter for the field lane.

setLane(Lane) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field lane.

setLane(Lane) - Method in class net.sourceforge.seqware.common.model.LaneAttribute

Setter for the field lane.

setLane(Lane) - Method in class net.sourceforge.seqware.common.model.LaneLink

Setter for the field lane.

setLane(Lane) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes

Setter for the field lane.

setLane(Lane) - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Setter for the field lane.

setLane(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId

Setter for the field lane.

setLane(Lane) - Method in class net.sourceforge.seqware.common.model.ShareLane

Setter for the field lane.

setLane(Integer) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

setLane1(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field lane1.

setLane2(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field lane2.

setLane3(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field lane3.

setLane4(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field lane4.

setLane5(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field lane5.

setLane6(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field lane6.

setLane7(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field lane7.

setLane8(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field lane8.

setLane_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Setter for the field lane_url.

setLaneAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Adds a new lane attribute if the tag does not exist for this lane, or changes the value of an existing lane attribute.

setLaneAttributeCollection(Collection<LaneAttribute>) - Method in class io.seqware.webservice.generated.model.Lane

setLaneAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.LaneAttribute

setLaneAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.LaneAttribute

Setter for the field laneAttributeId.

setLaneAttributes(Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field laneAttributes.

setLaneAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.LaneType

setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.LibrarySelection

setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.LibrarySource

setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.LibraryStrategy

setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.Organism

setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.Registration

setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.Sample

setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.SequencerRun

setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.StudyType

setLaneCount(int) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO

Setter for the field laneCount.

setLaneCycleDescriptor(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Set the value of laneCycleDescriptor

setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

Setter for the field laneDAO.

setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

setLaneDAO.

setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

Sets a private member variable with an instance of an implementation of LaneDAO.

setLaneDAO(LaneDAO) - Method in interface net.sourceforge.seqware.common.business.LaneService

setLaneDAO.

setLaneDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Set the value of laneDescription

setLaneForSequrncerRun(Lane, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setLaneForSequrncerRun.

setLaneForStudy(Lane, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setLaneForStudy.

setLaneId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport

setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.Ius

setLaneId(Integer) - Method in class io.seqware.webservice.generated.model.Lane

setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.LaneAttribute

setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.LaneLink

setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns

setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.ProcessingLanes

setLaneId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport

setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.ShareLane

setLaneId(Integer) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field laneId.

setLaneIndex(Integer) - Method in class io.seqware.webservice.generated.model.Lane

setLaneIndex(Integer) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field laneIndex.

setLaneLinkCollection(Collection<LaneLink>) - Method in class io.seqware.webservice.generated.model.Lane

setLaneLinkId(Integer) - Method in class io.seqware.webservice.generated.model.LaneLink

setLaneLinkId(int) - Method in class net.sourceforge.seqware.common.model.LaneLink

Setter for the field laneLinkId.

setLaneLinks(Set<LaneLink>) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field laneLinks.

setLaneName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Set the value of laneName

setLaneNumber(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Set the value of laneNumber, and sets the 'geo_lane' attribute.

setLanes(Set<Lane>) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field lanes.

setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field lanes.

setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field lanes.

setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field lanes.

setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field lanes.

setLanes(Set<LaneInfo>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of lanes

setLaneService(LaneService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.validation.LaneValidator

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Setter for the field laneService.

setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Setter for the field laneService.

setLanesForView(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.Sample

setLanesForView.

setLaneSkip(Boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Set the value of laneSkip

setLaneString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

setLaneSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

setLaneTypeId(Integer) - Method in class io.seqware.webservice.generated.model.LaneType

setLaneWorkflowRunsCollection(Collection<LaneWorkflowRuns>) - Method in class io.seqware.webservice.generated.model.Lane

setLaneWorkflowRunsCollection(Collection<LaneWorkflowRuns>) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setLaneWorkflowRunsId(Integer) - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns

setLastName(String) - Method in class io.seqware.webservice.generated.model.Registration

setLastName(String) - Method in class net.sourceforge.seqware.common.model.Registration

Setter for the field lastName.

setLastName(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto

Setter for the field lastName.

setLastUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Registration

setLatestDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport

Set the value of latestDate.

setLayout(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

setLayout(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Setter for the field layout.

setLength(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

setLength(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Setter for the field length.

setLibraryId(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto

Setter for the field libraryId.

setLibrarySamples(Collection<Sample>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Setter for the field librarySamples.

setLibrarySelection(LibrarySelection) - Method in class io.seqware.webservice.generated.model.Lane

setLibrarySelection(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.Lane

setLibrarySelectionAcc(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Set the value of librarySelectionAcc

setLibrarySelectionDAO(LibrarySelectionDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl

setLibrarySelectionDAO.

setLibrarySelectionDAO(LibrarySelectionDAO) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService

setLibrarySelectionDAO.

setLibrarySelectionId(Integer) - Method in class io.seqware.webservice.generated.model.LibrarySelection

setLibrarySelectionId(Integer) - Method in class net.sourceforge.seqware.common.model.LibrarySelection

Setter for the field librarySelectionId.

setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.seqware.common.ContextImpl

setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Setter for the field librarySelectionService.

setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController

Setter for the field librarySelectionService.

setLibraryService(LibraryService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field libraryService.

setLibrarySizeCode(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Sets the library size code and sets the 'geo_library_size_code' attribute.

setLibrarySource(LibrarySource) - Method in class io.seqware.webservice.generated.model.Lane

setLibrarySource(LibrarySource) - Method in class net.sourceforge.seqware.common.model.Lane

setLibrarySourceAcc(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Set the value of librarySourceAcc

setLibrarySourceDAO(LibrarySourceDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl

setLibrarySourceDAO.

setLibrarySourceDAO(LibrarySourceDAO) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService

setLibrarySourceDAO.

setLibrarySourceId(Integer) - Method in class io.seqware.webservice.generated.model.LibrarySource

setLibrarySourceId(Integer) - Method in class net.sourceforge.seqware.common.model.LibrarySource

Setter for the field librarySourceId.

setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.seqware.common.ContextImpl

setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Setter for the field librarySourceService.

setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController

Setter for the field librarySourceService.

setLibrarySourceTemplateType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Set the value of librarySourceTemplateType sets the 'geo_library_source_template_type' attribute.

setLibraryStrategy(LibraryStrategy) - Method in class io.seqware.webservice.generated.model.Lane

setLibraryStrategy(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.Lane

setLibraryStrategyAcc(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Set the value of libraryStrategyAcc

setLibraryStrategyDAO(LibraryStrategyDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl

setLibraryStrategyDAO.

setLibraryStrategyDAO(LibraryStrategyDAO) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService

setLibraryStrategyDAO.

setLibraryStrategyId(Integer) - Method in class io.seqware.webservice.generated.model.LibraryStrategy

setLibraryStrategyId(Integer) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy

Setter for the field libraryStrategyId.

setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.seqware.common.ContextImpl

setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Setter for the field libraryStrategyService.

setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController

Setter for the field libraryStrategyService.

setLibraryType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Sets the library type and sets the 'geo_library_type' attribute .

setLibraryType(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Setter for the field libraryType.

setLimsAdmin(boolean) - Method in class io.seqware.webservice.generated.model.Registration

setLIMSAdmin(boolean) - Method in class net.sourceforge.seqware.common.model.Registration

setLIMSAdmin.

setList(List<ExperimentLibraryDesign>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentLibraryDesignList

setList.

setList(List<Experiment>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList

setList.

setList(List<ExperimentSpotDesign>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignList

setList.

setList(List<ExperimentSpotDesignReadSpec>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignReadSpecList

setList.

setList(List<File>) - Method in class net.sourceforge.seqware.common.model.lists.FileList

setList.

setList(List<Integer>) - Method in class net.sourceforge.seqware.common.model.lists.IntegerList

setList.

setList(List<IUS>) - Method in class net.sourceforge.seqware.common.model.lists.IUSList

setList.

setList(List<Lane>) - Method in class net.sourceforge.seqware.common.model.lists.LaneList

setList.

setList(List<LibrarySelection>) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList

setList.

setList(List<LibrarySource>) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySourceList

setList.

setList(List<LibraryStrategy>) - Method in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList

setList.

setList(List<Organism>) - Method in class net.sourceforge.seqware.common.model.lists.OrganismList

setList.

setList(List<Platform>) - Method in class net.sourceforge.seqware.common.model.lists.PlatformList

setList.

setList(List<Processing>) - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList

setList.

setList(List<ReturnValue>) - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList

setList.

setList(List<Sample>) - Method in class net.sourceforge.seqware.common.model.lists.SampleList

setList.

setList(List<SequencerRun>) - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList

setList.

setList(List<Study>) - Method in class net.sourceforge.seqware.common.model.lists.StudyList

setList.

setList(List<StudyType>) - Method in class net.sourceforge.seqware.common.model.lists.StudyTypeList

setList.

setList(List<Workflow>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList

setList.

setList(List<WorkflowParam>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList

setList.

setList(List<WorkflowParamValue>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList

setList.

setList(Collection<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList

setList.

setList(List<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2

setList.

setLocal() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

setLocal(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

setLocal() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

Sets this job to run locally.

setLocal(boolean) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

Sets whether this job should run locally.

setLocal() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

setLocal(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

setMapred_job_tracker(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setMaxMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

setMaxMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command

setMaxMemory(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

set max memory

setMd5sum(String) - Method in class io.seqware.webservice.generated.model.File

setMd5sum(String) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field md5sum.

setMd5sum(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata

setMd5sum(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

setMd5sum(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto

Setter for the field md5sum.

setMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setMemReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field memReq.

setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

Setter for the field metadata.

setMetadata(Metadata) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface

Lets you set the metadata object

setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.module.Module

Setter for the field metadata.

setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin

Lets you set the metadata object

setMetadata(Metadata) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface

Lets you set the metadata object

setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld

Lets you set the metadata object

setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin

Lets you set the metadata object

setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin

Lets you set the metadata object

setMetadataOutputPrefix(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob

setMetadataOutputPrefix(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob

setMetadataWriteback(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

setMetadataWriteBack(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

need metadata writeback? user can override this setting by using --no-metadata or --metadata from command line

setMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

setMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

setMetaType(String) - Method in class io.seqware.webservice.generated.model.File

setMetaType(String) - Method in class io.seqware.webservice.generated.model.FileType

setMetaType(String) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field metaType.

setMetaType(String) - Method in class net.sourceforge.seqware.common.model.FileType

Setter for the field metaType.

setMetaType(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata

setMetaType(List<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

setMetaType(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto

Setter for the field metaType.

setMetaws(Metadata) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

setMimeType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

setName(String) - Method in class io.seqware.webservice.generated.model.Experiment

setName(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

setName(String) - Method in class io.seqware.webservice.generated.model.Ius

setName(String) - Method in class io.seqware.webservice.generated.model.Lane

setName(String) - Method in class io.seqware.webservice.generated.model.LaneType

setName(String) - Method in class io.seqware.webservice.generated.model.LibrarySelection

setName(String) - Method in class io.seqware.webservice.generated.model.LibrarySource

setName(String) - Method in class io.seqware.webservice.generated.model.LibraryStrategy

setName(String) - Method in class io.seqware.webservice.generated.model.Organism

setName(String) - Method in class io.seqware.webservice.generated.model.Platform

setName(String) - Method in class io.seqware.webservice.generated.model.Sample

setName(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setName(String) - Method in class io.seqware.webservice.generated.model.StudyType

setName(String) - Method in class io.seqware.webservice.generated.model.Workflow

setName(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setName(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.model.LibrarySelection

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.model.LibrarySource

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.model.Organism

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.model.Platform

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.model.StudyType

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Set the value of name

setName(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

set the workflow name

setName(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

setName(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Setter for the field name.

setName(String) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto

Setter for the field name.

setName(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel

setNameNode(String) - Method in class net.sourceforge.seqware.common.business.UploadFile

Setter for the field nameNode.

setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile

setNamespace.

setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement

setNcbiTaxid(Integer) - Method in class io.seqware.webservice.generated.model.Organism

setNcbiTaxId(Integer) - Method in class net.sourceforge.seqware.common.model.Organism

Setter for the field ncbiTaxId.

setNcbiTaxonomyId(Integer) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto

Setter for the field ncbiTaxonomyId.

setNetwork(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setNetworkReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field networkReq.

setNewType(String) - Method in class io.seqware.webservice.generated.model.Study

setNewType(String) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field newType.

SetNodeIdInSession - Class in net.sourceforge.solexatools.util

SetNodeIdInSession class.

SetNodeIdInSession() - Constructor for class net.sourceforge.solexatools.util.SetNodeIdInSession

setNominalLength(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

setNominalLength(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Setter for the field nominalLength.

setNominalSdev(Double) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

setNominalSdev(Long) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Setter for the field nominalSdev.

setNotes(String) - Method in class io.seqware.webservice.generated.model.Invoice

setNotes(String) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field notes.

setNotRunned(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Setter for the field notRunned.

setOffspringProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field offspringProcessings.

setOkTo(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

setOOZIE_APP_PATH(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setOOZIE_APP_ROOT(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setOOZIE_JOBTRACKER(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setOOZIE_NAMENODE(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setOOZIE_QUEUENAME(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setOOZIE_URL(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setOOZIE_WORK_DIR(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

SetOperations - Class in net.sourceforge.seqware.pipeline.tools

Taken from http://www.java2s.com/Code/Java/Collections-Data-Structure/Setoperationsunionintersectiondifferencesymmetricdifferenceissubsetissuperset.htm

SetOperations() - Constructor for class net.sourceforge.seqware.pipeline.tools.SetOperations

setOrganism(String) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field organism.

setOrganism(Organism) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field organism.

setOrganism(OrganismDto) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Setter for the field organism.

setOrganismDAO(OrganismDAO) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl

setOrganismDAO.

setOrganismDAO(OrganismDAO) - Method in interface net.sourceforge.seqware.common.business.OrganismService

setOrganismDAO.

setOrganismId(Organism) - Method in class io.seqware.webservice.generated.model.Lane

setOrganismId(Integer) - Method in class io.seqware.webservice.generated.model.Organism

setOrganismId(Organism) - Method in class io.seqware.webservice.generated.model.Sample

setOrganismId(Integer) - Method in class net.sourceforge.seqware.common.model.Organism

Setter for the field organismId.

setOrganismId(Integer) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field organismId.

setOrganismId(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Sets the organismId, as long as the organism id is over 0.

setOrganismService(OrganismService) - Method in class net.sourceforge.seqware.common.ContextImpl

setOrganismService(OrganismService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController

Setter for the field organismService.

setOrganismService(OrganismService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController

Setter for the field organismService.

setOriginalFileName(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Setter for the field originalFileName.

setOs(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

Setter for the field outputDir.

setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob

setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob

setOutputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Setter for the field outputFiles.

setOutputLineCapacity(Integer) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command

Set the number of lines of stdout and stderr to output

setOutputPath(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field owner.

setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field owner.

setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field owner.

setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field owner.

setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field owner.

setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field owner.

setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field owner.

setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field owner.

setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field owner.

setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field owner.

setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field owner.

setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field owner.

setOwner(OwnerDto) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Setter for the field owner.

setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Experiment

setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.File

setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Invoice

setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Ius

setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Lane

setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Processing

setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Sample

setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.SequencerRun

setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Study

setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Workflow

setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setOwnerUserName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

setPage(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid

Setter for the field page.

setPaidAmount(BigInteger) - Method in class io.seqware.webservice.generated.model.Invoice

setPaidAmount(Double) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field paidAmount.

setPairedEnd(Boolean) - Method in class io.seqware.webservice.generated.model.SequencerRun

setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field pairedEnd.

setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field pairedEnd.

setPairedEnd(boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of pairedEnd

setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

setPairedFilePath(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setPairedFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field pairedFilePath.

setPairedFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field pairedFilePath.

setPairedOrientation(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

setPairedOrientation(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Setter for the field pairedOrientation.

setParameters(String) - Method in class io.seqware.webservice.generated.model.Processing

setParameters(String) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field parameters.

setParameters(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field parameters.

setParameters(List<String>) - Method in class net.sourceforge.seqware.pipeline.module.Module

setParameters.

setParameters(List<String>) - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface

setParameters.

setParams(List<String>) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface

Lets you set a List of params so the plugin can deal with parameters

setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin

Lets you set a List of params so the plugin can deal with parameters

setParams(List<String>) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface

Lets you set a List of params so the plugin can deal with parameters

setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld

Lets you set a List of params so the plugin can deal with parameters

setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin

Lets you set a List of params so the plugin can deal with parameters

setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin

Lets you set a List of params so the plugin can deal with parameters

setParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.solexatools.util.SummaryLine

Setter for the field params.

setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

setParentAccessions(Collection<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

set parent accessiosns for the job

setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

set the parent accessions for provision file job

setParentId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingRelationship

setParentId(Sample) - Method in class io.seqware.webservice.generated.model.SampleRelationship

setParentId(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy

setParentProcessingAccession(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

setParentProcessingAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

Setter for the field parentProcessingAccession.

setParentProcessings(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Setter for the field parentProcessings.

setParents(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field parents.

setParents(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field parents.

setParents(Collection<Job>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

set parent jobs

setParentUrls(Set<String>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Setter for the field parentUrls.

setParentWorkflowAccessions(Set<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

setPassword(String) - Method in class io.seqware.webservice.generated.model.Registration

setPassword(String) - Method in class net.sourceforge.seqware.common.model.Registration

Setter for the field password.

setPasswordHint(String) - Method in class io.seqware.webservice.generated.model.Registration

setPasswordHint(String) - Method in class net.sourceforge.seqware.common.model.Registration

Setter for the field passwordHint.

setPathToFirstFile(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field pathToFirstFile.

setPathToSecondFile(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field pathToSecondFile.

setPayee(boolean) - Method in class io.seqware.webservice.generated.model.Registration

setPayee(boolean) - Method in class net.sourceforge.seqware.common.model.Registration

Setter for the field payee.

setPeakMemory(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

set the max memory for the workflow

setPeakThreads(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

set the max threads for the workflow

setPegasusConfigDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setPending(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Setter for the field pending.

setPermanentBundleLocation(String) - Method in class io.seqware.webservice.generated.model.Workflow

setPermanentBundleLocation(String) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field permanentBundleLocation.

setPermBundleLocation(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field permBundleLocation.

setPfn(Pfn) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field platform.

setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field platform.

setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field platform.

setPlatformDAO(PlatformDAO) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl

setPlatformDAO.

setPlatformDAO(PlatformDAO) - Method in interface net.sourceforge.seqware.common.business.PlatformService

setPlatformDAO.

setPlatformId(Platform) - Method in class io.seqware.webservice.generated.model.Experiment

setPlatformId(Integer) - Method in class io.seqware.webservice.generated.model.Platform

setPlatformId(Platform) - Method in class io.seqware.webservice.generated.model.SequencerRun

setPlatformId(Integer) - Method in class net.sourceforge.seqware.common.model.Platform

Setter for the field platformId.

setPlatformId(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

setPlatformInt(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field platformInt.

setPlatformInt(int) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field platformInt.

setPlatformService(PlatformService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field platformService.

setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Setter for the field platformService.

setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController

Setter for the field platformService.

setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Setter for the field platformService.

setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController

Setter for the field platformService.

setPricePerUnit(BigInteger) - Method in class io.seqware.webservice.generated.model.Expense

setPricePerUnit(Double) - Method in class net.sourceforge.seqware.common.model.Expense

Setter for the field pricePerUnit.

setPrivate(boolean) - Method in class net.sourceforge.seqware.common.model.Workflow

setPrivate.

setProcCountInfo(List<SequencerRun>) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

setProcCountInfo.

setProcCountInfo(List<SequencerRun>) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

setProcCountInfo.

setProcess(Boolean) - Method in class io.seqware.webservice.generated.model.SequencerRun

setProcess(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field process.

setProcessedCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field processedCount.

setProcessExitStatus(Integer) - Method in class io.seqware.webservice.generated.model.Processing

setProcessExitStatus(Integer) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field processExitStatus.

setProcessExitStatus(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field processExitStatus.

setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.FileReportRow

Setter for the field processing.

setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

Setter for the field processing.

setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments

Setter for the field processing.

setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingIus

Setter for the field processing.

setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes

Setter for the field processing.

setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples

Setter for the field processing.

setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Setter for the field processing.

setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies

Setter for the field processing.

setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ShareProcessing

Setter for the field processing.

setProcessingAccession(int) - Method in class net.sourceforge.seqware.pipeline.module.Module

Setter for the field processingAccession.

setProcessingAttributeCollection(Collection<ProcessingAttribute>) - Method in class io.seqware.webservice.generated.model.Processing

setProcessingAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute

setProcessingAttributeId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

Setter for the field processingAttributeId.

setProcessingAttributes(Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field processingAttributes.

setProcessingByChildId(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship

Setter for the field processingByChildId.

setProcessingByParentId(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship

Setter for the field processingByParentId.

setProcessingCollection(Collection<Processing>) - Method in class io.seqware.webservice.generated.model.Registration

setProcessingCollection(Collection<Processing>) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setProcessingCollection1(Collection<Processing>) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setProcessingCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field processingCount.

setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

Setter for the field processingDAO.

setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

Sets a private member variable with an instance of an implementation of ProcessingDAO.

setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

setProcessingDAO.

setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

Setter for the field processingDAO.

setProcessingDAO(ProcessingDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

setProcessingDAO.

setProcessingExperimentsCollection(Collection<ProcessingExperiments>) - Method in class io.seqware.webservice.generated.model.Experiment

setProcessingExperimentsCollection(Collection<ProcessingExperiments>) - Method in class io.seqware.webservice.generated.model.Processing

setProcessingExperimentsDAO(ProcessingExperimentsDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl

setProcessingExperimentsDAO.

setProcessingExperimentsDAO(ProcessingExperimentsDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService

setProcessingExperimentsDAO.

setProcessingExperimentsId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

setProcessingExperimentsId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments

Setter for the field processingExperimentsId.

setProcessingExperimentsService(ProcessingExperimentsService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field processingExperimentsService.

setProcessingFilesCollection(Collection<ProcessingFiles>) - Method in class io.seqware.webservice.generated.model.File

setProcessingFilesCollection(Collection<ProcessingFiles>) - Method in class io.seqware.webservice.generated.model.Processing

setProcessingFilesId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingFiles

setProcessingForSequrncerRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setProcessingForSequrncerRun.

setProcessingForStudy(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setProcessingForStudy.

setProcessingForWorkflowRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setProcessingForWorkflowRun.

setProcessingForWorkflowRunRunning(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setProcessingForWorkflowRunRunning.

setProcessingId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport

setProcessingId(Integer) - Method in class io.seqware.webservice.generated.model.Processing

setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute

setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingFiles

setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingIus

setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingLanes

setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingSamples

setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingStudies

setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ShareProcessing

setProcessingId(Integer) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field processingId.

setProcessingIusCollection(Collection<ProcessingIus>) - Method in class io.seqware.webservice.generated.model.Ius

setProcessingIusCollection(Collection<ProcessingIus>) - Method in class io.seqware.webservice.generated.model.Processing

setProcessingIUSDAO(ProcessingIUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl

setProcessingIUSDAO.

setProcessingIUSDAO(ProcessingIUSDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService

setProcessingIUSDAO.

setProcessingIusId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingIus

setProcessingIusId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingIus

Setter for the field processingIusId.

setProcessingIusService(ProcessingIUSService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field processingIusService.

setProcessingLanesCollection(Collection<ProcessingLanes>) - Method in class io.seqware.webservice.generated.model.Lane

setProcessingLanesCollection(Collection<ProcessingLanes>) - Method in class io.seqware.webservice.generated.model.Processing

setProcessingLanesDAO(ProcessingLanesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl

setProcessingLanesDAO.

setProcessingLanesDAO(ProcessingLanesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService

setProcessingLanesDAO.

setProcessingLaneService(ProcessingLanesService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field processingLaneService.

setProcessingLanesId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingLanes

setProcessingLanesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes

Setter for the field processingLanesId.

setProcessingRelationshipCollection(Collection<ProcessingRelationship>) - Method in class io.seqware.webservice.generated.model.Processing

setProcessingRelationshipCollection1(Collection<ProcessingRelationship>) - Method in class io.seqware.webservice.generated.model.Processing

setProcessingRelationshipDAO(ProcessingRelationshipDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl

setProcessingRelationshipDAO.

setProcessingRelationshipDAO(ProcessingRelationshipDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService

setProcessingRelationshipDAO.

setProcessingRelationshipId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingRelationship

setProcessingRelationshipId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship

Setter for the field processingRelationshipId.

setProcessingRelationshipService(ProcessingRelationshipService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field processingRelationshipService.

setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field processings.

setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field processings.

setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field processings.

setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field processings.

setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field processings.

setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field processings.

setProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field processings.

setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field processings.

setProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field processings.

setProcessingSamplesCollection(Collection<ProcessingSamples>) - Method in class io.seqware.webservice.generated.model.Processing

setProcessingSamplesCollection(Collection<ProcessingSamples>) - Method in class io.seqware.webservice.generated.model.Sample

setProcessingSamplesDAO(ProcessingSamplesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl

setProcessingSamplesDAO.

setProcessingSamplesDAO(ProcessingSamplesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService

setProcessingSamplesDAO.

setProcessingSamplesId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingSamples

setProcessingSamplesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples

Setter for the field processingSamplesId.

setProcessingSamplesService(ProcessingSamplesService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field processingSamplesService.

setProcessingSequencerRunsCollection(Collection<ProcessingSequencerRuns>) - Method in class io.seqware.webservice.generated.model.Processing

setProcessingSequencerRunsCollection(Collection<ProcessingSequencerRuns>) - Method in class io.seqware.webservice.generated.model.SequencerRun

setProcessingSequencerRunsDAO(ProcessingSequencerRunsDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl

setProcessingSequencerRunsDAO.

setProcessingSequencerRunsDAO(ProcessingSequencerRunsDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService

setProcessingSequencerRunsDAO.

setProcessingSequencerRunService(ProcessingSequencerRunsService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field processingSequencerRunService.

setProcessingSequencerRunsId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

setProcessingSequencerRunsId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Setter for the field processingSequencerRunsId.

setProcessingService(ProcessingService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Setter for the field processingService.

setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Setter for the field processingService.

setProcessingsForView(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Lane

setProcessingsForView.

setProcessingStudiesCollection(Collection<ProcessingStudies>) - Method in class io.seqware.webservice.generated.model.Processing

setProcessingStudiesCollection(Collection<ProcessingStudies>) - Method in class io.seqware.webservice.generated.model.Study

setProcessingStudiesDAO(ProcessingStudiesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl

setProcessingStudiesDAO.

setProcessingStudiesDAO(ProcessingStudiesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService

setProcessingStudiesDAO.

setProcessingStudiesId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingStudies

setProcessingStudiesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies

Setter for the field processingStudiesId.

setProcessingStudiesService(ProcessingStudiesService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field processingStudiesService.

setProjectCode(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

setProjectId(int) - Method in class io.seqware.webservice.generated.model.Study

setProjectId(Integer) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field projectId.

setPublic(boolean) - Method in class net.sourceforge.seqware.common.model.Workflow

setPublic.

setQsubOptions(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

Allows specifying options to qsub.

setQualityMultiplier(Integer) - Method in class io.seqware.webservice.generated.model.Experiment

setQualityMultiplier(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field qualityMultiplier.

setQualityNumberOfLevels(Integer) - Method in class io.seqware.webservice.generated.model.Experiment

setQualityNumberOfLevels(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field qualityNumberOfLevels.

setQualityScorer(String) - Method in class io.seqware.webservice.generated.model.Experiment

setQualityScorer(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setQualityScorer(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field qualityScorer.

setQualityType(String) - Method in class io.seqware.webservice.generated.model.Experiment

setQualityType(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field qualityType.

setQueue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

setQueue(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

set the queue

setQueue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

setRandom(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

set the pre-defined random variable

setReadClass(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

setReadClass(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Setter for the field readClass.

setReader(BufferedReader) - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread

Setter for the field reader.

setReadIndex(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

setReadIndex(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Setter for the field readIndex.

setReadLabel(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

setReadLabel(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Setter for the field readLabel.

setReadSpec(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

setReadSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Setter for the field readSpec.

setReadSpecs(SortedSet<ExperimentSpotDesignReadSpec>) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Setter for the field readSpecs.

setReadsPerSpot(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

setReadsPerSpot(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Setter for the field readsPerSpot.

setReadType(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

setReadType(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

Setter for the field readType.

setReadyToProcess(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field readyToProcess.

setRefLane(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun

setRefLane(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field refLane.

setRefLane(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field refLane.

setRegions(String) - Method in class io.seqware.webservice.generated.model.Lane

setRegions(String) - Method in class io.seqware.webservice.generated.model.Sample

setRegions(String) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field regions.

setRegions(String) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field regions.

setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareExperiment

Setter for the field registration.

setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareFile

Setter for the field registration.

setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareLane

Setter for the field registration.

setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareProcessing

Setter for the field registration.

setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareSample

Setter for the field registration.

setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareStudy

Setter for the field registration.

setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

Setter for the field registration.

setRegistrationDAO(RegistrationDAO) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl

setRegistrationDAO.

setRegistrationDAO(RegistrationDAO) - Method in interface net.sourceforge.seqware.common.business.RegistrationService

setRegistrationDAO.

setRegistrationId(Integer) - Method in class io.seqware.webservice.generated.model.Registration

setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareExperiment

setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareFile

setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareLane

setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareProcessing

setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareSample

setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareStudy

setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

setRegistrationId(Integer) - Method in class net.sourceforge.seqware.common.model.Registration

Setter for the field registrationId.

setRegistrationService(RegistrationService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field registrationService.

setRegistrationService(RegistrationService) - Static method in class net.sourceforge.seqware.webservice.resources.BasicResource

Setter for the field registrationService.

setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController

Setter for the field registrationService.

setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController

Setter for the field registrationService.

setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController

Setter for the field registrationService.

setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.LoginController

Setter for the field registrationService.

setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController

Setter for the field registrationService.

setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController

Setter for the field registrationService.

setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController

Setter for the field registrationService.

setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController

Setter for the field registrationService.

setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

Setter for the field registrationService.

setRelationship(String) - Method in class io.seqware.webservice.generated.model.ProcessingRelationship

setRelationship(String) - Method in class io.seqware.webservice.generated.model.SampleRelationship

setRelationship(String) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship

Setter for the field relationship.

setReportInputFiles(boolean) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

setRequireFiles(boolean) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Setter for the field requireFiles.

setRequirements(Collection<Requirement>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

setReturnValue(ReturnValue) - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException

Setter for the field returnValue.

setReturnValue(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field returnValue.

setRootProcessingName(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

setRootProcessingSwa(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

setRootSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Setter for the field rootSample.

setRowId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport

setRowId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport

setRowId(Integer) - Method in class net.sourceforge.seqware.common.model.FileReportRow

Setter for the field rowId.

setRowId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Setter for the field rowId.

setRows(List<Flexigrid.Cells>) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid

Setter for the field rows.

setRunAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Adds a new run attribute if the tag does not exist for this run, or changes the value of an existing run attribute.

setRunAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of runAttributes

setRunCenter(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setRunCenter(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field runCenter.

setRunCenter(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field runCenter.

setRunDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of runDescription

setRunFilePath(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of runFilePath

setRunName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of runName

setRunSkip(boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of runSkip

setRunStartTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field runStartTimestamp.

setRunStartTstmp(Date) - Method in class io.seqware.webservice.generated.model.Processing

setRunStartTstmp(Date) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field runStartTstmp.

setRunStopTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field runStopTimestamp.

setRunStopTstmp(Date) - Method in class io.seqware.webservice.generated.model.Processing

setRunStopTstmp(Date) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field runStopTstmp.

setSample(Sample) - Method in class net.sourceforge.seqware.common.model.FileReportRow

Setter for the field sample.

setSample(Sample) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field sample.

setSample(Sample) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field sample.

setSample(Sample) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples

Setter for the field sample.

setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleAttribute

Setter for the field sample.

setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleLink

Setter for the field sample.

setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleSearch

Setter for the field sample.

setSample(Sample) - Method in class net.sourceforge.seqware.common.model.ShareSample

Setter for the field sample.

setSample(Sample) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field sample.

setSample(Sample) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Setter for the field sample.

setSample(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

setSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Setter for the field sample.

setSample_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Setter for the field sample_url.

setSampleAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Adds a new sample attribute if the tag does not exist for this sample, or changes the value of an existing sample attribute.

setSampleAttributeCollection(Collection<SampleAttribute>) - Method in class io.seqware.webservice.generated.model.Sample

setSampleAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.SampleAttribute

setSampleAttributeId(int) - Method in class net.sourceforge.seqware.common.model.SampleAttribute

Setter for the field sampleAttributeId.

setSampleAttributes(Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field sampleAttributes.

setSampleAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Set the value of sampleAttributes

setSampleCode(String) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field sampleCode.

setSampleCollection(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Experiment

setSampleCollection(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Organism

setSampleCollection(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Registration

setSampleCollection(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Sample

setSampleCollection1(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Sample

setSampleDAO(SampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

Setter for the field sampleDAO.

setSampleDAO(SampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

setSampleDAO.

setSampleDAO(SampleDAO) - Method in interface net.sourceforge.seqware.common.business.SampleService

setSampleDAO.

setSampleDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Set the value of sampleDescription

setSampleForStudy(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setSampleForStudy.

setSampleForWorkflowRun(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setSampleForWorkflowRun.

setSampleForWorkflowRunRunning(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setSampleForWorkflowRunRunning.

setSampleHierarchies(List<SampleHierarchy>) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchies

setSampleId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport

setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.Ius

setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.Lane

setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.ProcessingSamples

setSampleId(Integer) - Method in class io.seqware.webservice.generated.model.Sample

setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.SampleAttribute

setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.SampleLink

setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.SampleSearch

setSampleId(SequencerRun) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute

setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.ShareSample

setSampleId(Integer) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field sampleId.

setSampleId(Integer) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field sampleId.

setSampleId(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy

setSampleId(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto

Setter for the field sampleId.

setSampleLinkCollection(Collection<SampleLink>) - Method in class io.seqware.webservice.generated.model.Sample

setSampleLinkId(Integer) - Method in class io.seqware.webservice.generated.model.SampleLink

setSampleLinkId(int) - Method in class net.sourceforge.seqware.common.model.SampleLink

Setter for the field sampleLinkId.

setSampleLinks(Set<SampleLink>) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field sampleLinks.

setSampleRelationshipCollection(Collection<SampleRelationship>) - Method in class io.seqware.webservice.generated.model.Sample

setSampleRelationshipCollection1(Collection<SampleRelationship>) - Method in class io.seqware.webservice.generated.model.Sample

setSampleRelationshipId(Integer) - Method in class io.seqware.webservice.generated.model.SampleRelationship

setSampleReportDAO(SampleReportDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl

Setter for the field sampleReportDAO.

setSampleReportService(SampleReportService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field sampleReportService.

setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Setter for the field sampleReportService.

setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController

Setter for the field sampleReportService.

setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Setter for the field sampleReportService.

setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field samples.

setSamples(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field samples.

setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field samples.

setSamples(Set<SampleInfo>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Set the value of samples

setSampleSearch(SampleSearch) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute

Setter for the field sampleSearch.

setSampleSearchAttributeCollection(Collection<SampleSearchAttribute>) - Method in class io.seqware.webservice.generated.model.SampleSearch

setSampleSearchAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute

setSampleSearchAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute

Setter for the field sampleSearchAttributeId.

setSampleSearchAttributes(Set<SampleSearchAttribute>) - Method in class net.sourceforge.seqware.common.model.SampleSearch

Setter for the field sampleSearchAttributes.

setSampleSearchCollection(Collection<SampleSearch>) - Method in class io.seqware.webservice.generated.model.Sample

setSampleSearchId(Integer) - Method in class io.seqware.webservice.generated.model.SampleSearch

setSampleSearchId(SampleSearch) - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute

setSampleSearchId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleSearch

Setter for the field sampleSearchId.

setSampleService(SampleService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.validation.SampleValidator

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Setter for the field sampleService.

setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController

Setter for the field sampleService.

setSampleSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

setSampleType(String) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field sampleType.

setSampleUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto

Setter for the field sampleUrl.

setScientificName(String) - Method in class io.seqware.webservice.generated.model.Sample

setSelection(LibrarySelection) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

setSelection(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Setter for the field selection.

setSender(MailSender) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController

Setter for the field sender.

setSequencer_run_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Setter for the field sequencer_run_url.

setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field sequencerRun.

setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Setter for the field sequencerRun.

setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Setter for the field sequencerRun.

setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId

Setter for the field sequencerRun.

setSequencerRun(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

setSequencerRun(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setSequencerRun.

setSequencerRunAttributeCollection(Collection<SequencerRunAttribute>) - Method in class io.seqware.webservice.generated.model.SequencerRun

setSequencerRunAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute

setSequencerRunAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

Setter for the field sequencerRunAttributeId.

setSequencerRunAttributes(Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field sequencerRunAttributes.

setSequencerRunCollection(Collection<SequencerRun>) - Method in class io.seqware.webservice.generated.model.Platform

setSequencerRunCollection(Collection<SequencerRun>) - Method in class io.seqware.webservice.generated.model.Registration

setSequencerRunDAO(SequencerRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

Setter for the field sequencerRunDAO.

setSequencerRunDAO(SequencerRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

setSequencerRunDAO.

setSequencerRunDAO(SequencerRunDAO) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

setSequencerRunDAO.

setSequencerRunId(SequencerRun) - Method in class io.seqware.webservice.generated.model.Lane

setSequencerRunId(SequencerRun) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

setSequencerRunId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport

setSequencerRunId(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun

setSequencerRunId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field sequencerRunId.

setSequencerRunId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field sequencerRunId.

setSequencerRuns(Set<SequencerRun>) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field sequencerRuns.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Setter for the field sequencerRunService.

setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController

Setter for the field sequencerRunService.

setSequencerRunSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

setSequencerRunValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Setter for the field sequencerRunValidator.

setSequencerRunWizardDTO(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

setSequencerRunWizardDTO.

setSequencerRunWizardValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController

Setter for the field sequencerRunWizardValidator.

setSequenceSpace(String) - Method in class io.seqware.webservice.generated.model.Experiment

setSequenceSpace(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field sequenceSpace.

setSeqwareAccession(Integer) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

setSeqwareAccessionString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

setSeqwareRevision(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setSeqwareRevision(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field seqwareRevision.

setSeqwareVersion(String) - Method in class io.seqware.webservice.generated.model.Workflow

setSeqwareVersion(String) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field seqwareVersion.

setSessionFactory(SessionFactory) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field sessionFactory.

setSharedStudies(SortedSet<ShareStudy>) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field sharedStudies.

setSharedWorkflowRuns(SortedSet<ShareWorkflowRun>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field sharedWorkflowRuns.

setShareExperimentCollection(Collection<ShareExperiment>) - Method in class io.seqware.webservice.generated.model.Experiment

setShareExperimentCollection(Collection<ShareExperiment>) - Method in class io.seqware.webservice.generated.model.Registration

setShareExperimentDAO(ShareExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl

setShareExperimentDAO.

setShareExperimentDAO(ShareExperimentDAO) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService

setShareExperimentDAO.

setShareExperimentId(Integer) - Method in class io.seqware.webservice.generated.model.ShareExperiment

setShareExperimentId(int) - Method in class net.sourceforge.seqware.common.model.ShareExperiment

Setter for the field shareExperimentId.

setShareFileCollection(Collection<ShareFile>) - Method in class io.seqware.webservice.generated.model.File

setShareFileCollection(Collection<ShareFile>) - Method in class io.seqware.webservice.generated.model.Registration

setShareFileDAO(ShareFileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl

setShareFileDAO.

setShareFileDAO(ShareFileDAO) - Method in interface net.sourceforge.seqware.common.business.ShareFileService

setShareFileDAO.

setShareFileId(Integer) - Method in class io.seqware.webservice.generated.model.ShareFile

setShareFileId(int) - Method in class net.sourceforge.seqware.common.model.ShareFile

Setter for the field shareFileId.

setShareLaneCollection(Collection<ShareLane>) - Method in class io.seqware.webservice.generated.model.Lane

setShareLaneCollection(Collection<ShareLane>) - Method in class io.seqware.webservice.generated.model.Registration

setShareLaneDAO(ShareLaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl

setShareLaneDAO.

setShareLaneDAO(ShareLaneDAO) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService

setShareLaneDAO.

setShareLaneId(Integer) - Method in class io.seqware.webservice.generated.model.ShareLane

setShareLaneId(int) - Method in class net.sourceforge.seqware.common.model.ShareLane

Setter for the field shareLaneId.

setShareProcessingCollection(Collection<ShareProcessing>) - Method in class io.seqware.webservice.generated.model.Processing

setShareProcessingCollection(Collection<ShareProcessing>) - Method in class io.seqware.webservice.generated.model.Registration

setShareProcessingDAO(ShareProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl

setShareProcessingDAO.

setShareProcessingDAO(ShareProcessingDAO) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService

setShareProcessingDAO.

setShareProcessingId(Integer) - Method in class io.seqware.webservice.generated.model.ShareProcessing

setShareProcessingId(int) - Method in class net.sourceforge.seqware.common.model.ShareProcessing

Setter for the field shareProcessingId.

setShareSampleCollection(Collection<ShareSample>) - Method in class io.seqware.webservice.generated.model.Registration

setShareSampleCollection(Collection<ShareSample>) - Method in class io.seqware.webservice.generated.model.Sample

setShareSampleDAO(ShareSampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl

setShareSampleDAO.

setShareSampleDAO(ShareSampleDAO) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService

setShareSampleDAO.

setShareSampleId(Integer) - Method in class io.seqware.webservice.generated.model.ShareSample

setShareSampleId(int) - Method in class net.sourceforge.seqware.common.model.ShareSample

Setter for the field shareSampleId.

setShareStudyCollection(Collection<ShareStudy>) - Method in class io.seqware.webservice.generated.model.Registration

setShareStudyCollection(Collection<ShareStudy>) - Method in class io.seqware.webservice.generated.model.Study

setShareStudyDAO(ShareStudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl

setShareStudyDAO.

setShareStudyDAO(ShareStudyDAO) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService

setShareStudyDAO.

setShareStudyId(Integer) - Method in class io.seqware.webservice.generated.model.ShareStudy

setShareStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy

Setter for the field shareStudyId.

setShareStudyService(ShareStudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController

Setter for the field shareStudyService.

setShareStudyService(ShareStudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

Setter for the field shareStudyService.

setShareWorkflowRunCollection(Collection<ShareWorkflowRun>) - Method in class io.seqware.webservice.generated.model.Registration

setShareWorkflowRunCollection(Collection<ShareWorkflowRun>) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setShareWorkflowRunDAO(ShareWorkflowRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl

setShareWorkflowRunDAO.

setShareWorkflowRunDAO(ShareWorkflowRunDAO) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService

setShareWorkflowRunDAO.

setShareWorkflowRunId(Integer) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

setShareWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

Setter for the field shareWorkflowRunId.

setShareWorkflowRunService(ShareWorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController

Setter for the field shareWorkflowRunService.

setShareWorkflowRunService(ShareWorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController

Setter for the field shareWorkflowRunService.

setSite(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn

Setter for the field site.

setSize(BigInteger) - Method in class io.seqware.webservice.generated.model.File

setSize(Long) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field size.

setSize(Long) - Method in class net.sourceforge.seqware.common.module.FileMetadata

setSize(Long) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

setSize(Long) - Method in class net.sourceforge.seqware.webservice.dto.FileDto

Setter for the field size.

setSizeString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.File

setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.Ius

setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.Lane

setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.Sample

setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.SequencerRun

setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.File

setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field skip.

setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field skip.

setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field skip.

setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field skip.

setSkip(Boolean) - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Setter for the field skip.

setSkipIfMissing(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

setSlide1FilePath(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setSlide1LaneCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun

setSlide2FilePath(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setSlide2LaneCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun

setSlideCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun

setSlideOneFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field slideOneFilePath.

setSlideOneFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field slideOneFilePath.

setSlideOneLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field slideOneLaneCount.

setSlideOneLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field slideOneLaneCount.

setSlideTwoFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field slideTwoFilePath.

setSlideTwoFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field slideTwoFilePath.

setSlideTwoLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field slideTwoLaneCount.

setSlideTwoLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field slideTwoLaneCount.

setSortable(boolean) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel

setSortKeySample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Setter for the field sortKeySample.

setSource(LibrarySource) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

setSource(LibrarySource) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Setter for the field source.

setSourcePath(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

setSpotDesignReadSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field spotDesignReadSpec.

setStartDate(Date) - Method in class io.seqware.webservice.generated.model.Invoice

setStartDate(Date) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field startDate.

setStartPage(String) - Method in class net.sourceforge.solexatools.util.PageInfo

Setter for the field startPage.

setState(String) - Method in class io.seqware.webservice.generated.model.Invoice

setState(InvoiceState) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field state.

setStatus(String) - Method in class io.seqware.webservice.generated.model.Experiment

setStatus(String) - Method in class io.seqware.webservice.generated.model.Processing

setStatus(String) - Method in class io.seqware.webservice.generated.model.SampleReport

setStatus(String) - Method in class io.seqware.webservice.generated.model.SequencerRun

setStatus(String) - Method in class io.seqware.webservice.generated.model.Study

setStatus(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setStatus(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field status.

setStatus(ProcessingStatus) - Method in class net.sourceforge.seqware.common.model.Processing

setStatus(String) - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Setter for the field status.

setStatus(SequencerRunStatus) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field status.

setStatus(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field status.

setStatus(String) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field status.

setStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field status.

setStatus(SequencerRunStatus) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of the sequencer run status

setStatusCmd(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setStatusCmd(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field statusCmd.

setStatusCounts(int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools

Setter for the field statusCounts.

setStatuses(String[]) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Setter for the field statuses.

setStderr(String) - Method in class io.seqware.webservice.generated.model.Processing

setStderr(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setStderr(String) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field stderr.

setStdErr(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field stdErr.

setStderr(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field stderr.

setStderr(File) - Method in interface net.sourceforge.seqware.pipeline.module.RedirectAware

setStderr.

setStderrFile(File) - Method in class net.sourceforge.seqware.pipeline.module.Module

Added by Xiaoshu Wang: Setter for the file that will be used to redirect stderr

setStdout(String) - Method in class io.seqware.webservice.generated.model.Processing

setStdout(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setStdout(String) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field stdout.

setStdOut(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field stdOut.

setStdout(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field stdout.

setStdout(File) - Method in interface net.sourceforge.seqware.pipeline.module.RedirectAware

setStdout.

setStdoutFile(File) - Method in class net.sourceforge.seqware.pipeline.module.Module

Setter for the field stdoutFile.

setStrategy(LibraryStrategy) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

setStrategy(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

Setter for the field strategy.

setStrExpectedNumberReads(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field strExpectedNumberReads.

setStrExpectedNumberRuns(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field strExpectedNumberRuns.

setStrExpectedNumReads(String) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field strExpectedNumReads.

setStrExpectedNumRuns(String) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field strExpectedNumRuns.

setStrLaneCount(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO

Setter for the field strLaneCount.

setStrRefLane(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field strRefLane.

setStrStartURL(String) - Method in class net.sourceforge.seqware.common.business.UploadFile

Setter for the field strStartURL.

setStrStartURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field strStartURL.

setStudies(Set<Study>) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field studies.

setStudy(Study) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field study.

setStudy(Study) - Method in class net.sourceforge.seqware.common.model.FileReportRow

Setter for the field study.

setStudy(Study) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies

Setter for the field study.

setStudy(Study) - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Setter for the field study.

setStudy(Study) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId

Setter for the field study.

setStudy(Study) - Method in class net.sourceforge.seqware.common.model.StudyAttribute

Setter for the field study.

setStudy(Study) - Method in class net.sourceforge.seqware.common.model.StudyLink

Setter for the field study.

setStudy(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setStudy.

setStudyAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Adds a new study attribute if the tag does not exist for this study, or changes the value of an existing study attribute.

setStudyAttributeCollection(Collection<StudyAttribute>) - Method in class io.seqware.webservice.generated.model.Study

setStudyAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.StudyAttribute

setStudyAttributeId(int) - Method in class net.sourceforge.seqware.common.model.StudyAttribute

Setter for the field studyAttributeId.

setStudyAttributes(Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field studyAttributes.

setStudyAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of studyAttributes

setStudyCenterName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of studyCenterName

setStudyCenterProject(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of studyCenterProject

setStudyCollection(Collection<Study>) - Method in class io.seqware.webservice.generated.model.Registration

setStudyCollection(Collection<Study>) - Method in class io.seqware.webservice.generated.model.StudyType

setStudyDAO(StudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

Setter for the field studyDAO.

setStudyDAO(StudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

setStudyDAO.

setStudyDAO(StudyDAO) - Method in interface net.sourceforge.seqware.common.business.StudyService

setStudyDAO.

setStudyDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of studyDescription

setStudyId(Study) - Method in class io.seqware.webservice.generated.model.Experiment

setStudyId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport

setStudyId(Study) - Method in class io.seqware.webservice.generated.model.ProcessingStudies

setStudyId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport

setStudyId(Study) - Method in class io.seqware.webservice.generated.model.ShareStudy

setStudyId(Integer) - Method in class io.seqware.webservice.generated.model.Study

setStudyId(Study) - Method in class io.seqware.webservice.generated.model.StudyAttribute

setStudyId(Study) - Method in class io.seqware.webservice.generated.model.StudyLink

setStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy

Setter for the field studyId.

setStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field studyId.

setStudyLinkCollection(Collection<StudyLink>) - Method in class io.seqware.webservice.generated.model.Study

setStudyLinkId(Integer) - Method in class io.seqware.webservice.generated.model.StudyLink

setStudyLinkId(int) - Method in class net.sourceforge.seqware.common.model.StudyLink

Setter for the field studyLinkId.

setStudyLinks(Set<StudyLink>) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field studyLinks.

setStudyService(StudyService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.validation.StudyValidator

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyTableController

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyTableControllerDetails

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Setter for the field studyService.

setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Setter for the field studyService.

setStudySwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

setStudyTitle(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of studyTitle

setStudyType(StudyType) - Method in class io.seqware.webservice.generated.model.Lane

setStudyType(StudyType) - Method in class net.sourceforge.seqware.common.model.Lane

setStudyType(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

setStudyTypeAcc(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

Set the value of studyTypeAcc

setStudyTypeDAO(StudyTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

Setter for the field studyTypeDAO.

setStudyTypeDAO(StudyTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl

setStudyTypeDAO.

setStudyTypeDAO(StudyTypeDAO) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService

setStudyTypeDAO.

setStudyTypeId(Integer) - Method in class io.seqware.webservice.generated.model.StudyType

setStudyTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.StudyType

Setter for the field studyTypeId.

setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.seqware.common.ContextImpl

setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

Setter for the field studyTypeService.

setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController

Setter for the field studyTypeService.

setSummaryLines(List<SummaryLine>) - Method in class net.sourceforge.solexatools.util.SummaryData

Setter for the field summaryLines.

setSwa(Integer) - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Setter for the field swa.

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Expense

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Experiment

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.File

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Invoice

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Ius

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Lane

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Processing

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingIus

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingLanes

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingSamples

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingStudies

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Sample

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareExperiment

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareFile

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareLane

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareProcessing

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareSample

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareStudy

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Study

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Workflow

setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Expense

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingIus

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareExperiment

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareFile

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareLane

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareProcessing

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareSample

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field swAccession.

setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field swAccession.

setSwCluster(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment

setTag(String) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute

setTag(String) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute

setTag(String) - Method in class io.seqware.webservice.generated.model.FileAttribute

setTag(String) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute

setTag(String) - Method in class io.seqware.webservice.generated.model.Ius

setTag(String) - Method in class io.seqware.webservice.generated.model.IusAttribute

setTag(String) - Method in class io.seqware.webservice.generated.model.LaneAttribute

setTag(String) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute

setTag(String) - Method in class io.seqware.webservice.generated.model.SampleAttribute

setTag(String) - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute

setTag(String) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute

setTag(String) - Method in class io.seqware.webservice.generated.model.StudyAttribute

setTag(String) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute

setTag(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute

setTag(String) - Method in interface net.sourceforge.seqware.common.model.Attribute

setTag.

setTag(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

Setter for the field tag.

setTag(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute

setTag.

setTag(String) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field tag.

setTag(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute

setTag.

setTag(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute

Setter for the field tag.

setTag(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

setTag.

setTag(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute

setTag.

setTag(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute

setTag.

setTag(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

setTag.

setTag(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute

setTag.

setTag(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute

setTag.

setTag(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute

setTag.

setTag(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit

setTags(String) - Method in class io.seqware.webservice.generated.model.Lane

setTags(String) - Method in class io.seqware.webservice.generated.model.Sample

setTags(String) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field tags.

setTags(String) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field tags.

setTags(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

set the key-value properties from metadata.xml

setTagSpec(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

setTagSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

Setter for the field tagSpec.

setTargetedResequencing(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Set the value of targetedResequencing and sets the 'geo_targeted_resequencing' attribute.

setTaskGroup(Boolean) - Method in class io.seqware.webservice.generated.model.Processing

setTaskGroup(boolean) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field taskGroup.

setTaxonId(Integer) - Method in class io.seqware.webservice.generated.model.Sample

setTemplate(String) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field template.

setTemplate(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field template.

setTemplatePath(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field templatePath.

setTemplateType(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Setter for the field templateType.

setTest(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

setTestCmd(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field testCmd.

setThreads(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

setThreads(int) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job

set the max thread number

setThreads(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch

setTimeTaken(String) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Setter for the field timeTaken.

SETTINGSFILENOTFOUND - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant SETTINGSFILENOTFOUND=13

setTissSource(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Setter for the field tissSource.

setTissueOrigin(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Set the value of tissueOrigin and sets the 'geo_tissue_origin' attribute.

setTissuePreparation(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Set the value of tissuePreparation, and sets the 'geo_tissue_preparation' attribute.

setTissueType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

Set the value of tissueType and sets the 'geo_tissue_type' attribute.

setTitle(String) - Method in class io.seqware.webservice.generated.model.Experiment

setTitle(String) - Method in class io.seqware.webservice.generated.model.Sample

setTitle(String) - Method in class io.seqware.webservice.generated.model.Study

setTitle(String) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field title.

setTitle(String) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field title.

setTitle(String) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field title.

setTotal(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid

Setter for the field total.

setTotalPrice(BigInteger) - Method in class io.seqware.webservice.generated.model.Expense

setTotalPrice(Double) - Method in class net.sourceforge.seqware.common.model.Expense

Setter for the field totalPrice.

setTotalUnits(BigInteger) - Method in class io.seqware.webservice.generated.model.Expense

setTotalUnits(Double) - Method in class net.sourceforge.seqware.common.model.Expense

Setter for the field totalUnits.

setType(String) - Method in class io.seqware.webservice.generated.model.File

setType(LaneType) - Method in class io.seqware.webservice.generated.model.Lane

setType(String) - Method in class io.seqware.webservice.generated.model.Sample

setType(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam

setType(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

setType(String) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field type.

setType(String) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field type.

setType(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field type.

setType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Setter for the field type.

setType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

Setter for the field type.

setType(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata

setType(Requirement.Type) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement

setType(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

setType(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto

Setter for the field type.

setType(String) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController

Setter for the field type.

setTypeNode(String) - Method in class net.sourceforge.seqware.common.business.UploadFile

Setter for the field typeNode.

setUnit(String) - Method in class io.seqware.webservice.generated.model.FileAttribute

setUnit(String) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute

setUnit(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute

setUnit(String) - Method in interface net.sourceforge.seqware.common.model.Attribute

setUnit.

setUnit(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

setUnit(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute

setUnit.

setUnit(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute

setUnit.

setUnit(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute

setUnit(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

setUnit.

setUnit(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute

setUnit.

setUnit(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute

setUnit.

setUnit(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

setUnit.

setUnit(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute

setUnit.

setUnit(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute

setUnit.

setUnit(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute

setUnit.

setUnit(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit

setUnit(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto

Setter for the field unit.

setUnits(String) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute

setUnits(String) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute

setUnits(String) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute

setUnits(String) - Method in class io.seqware.webservice.generated.model.IusAttribute

setUnits(String) - Method in class io.seqware.webservice.generated.model.LaneAttribute

setUnits(String) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute

setUnits(String) - Method in class io.seqware.webservice.generated.model.SampleAttribute

setUnits(String) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute

setUnits(String) - Method in class io.seqware.webservice.generated.model.StudyAttribute

setUnits(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

Setter for the field units.

setUnits(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute

Setter for the field units.

setUnits(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute

Setter for the field units.

setUnits(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

Setter for the field units.

setUnits(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute

Setter for the field units.

setUnits(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

Setter for the field units.

setUnits(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute

Setter for the field units.

setup(String) - Static method in class net.sourceforge.seqware.common.util.freemarker.Freemarker

setup.

setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Experiment

Setter for the field updateTimestamp.

setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field updateTimestamp.

setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field updateTimestamp.

setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field updateTimestamp.

setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Registration

Setter for the field updateTimestamp.

setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Sample

Setter for the field updateTimestamp.

setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field updateTimestamp.

setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field updateTimestamp.

setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareStudy

Setter for the field updateTimestamp.

setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

Setter for the field updateTimestamp.

setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Study

Setter for the field updateTimestamp.

setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field updateTimestamp.

setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field updateTimestamp.

setUpdateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Setter for the field updateTimeStamp.

setUpdateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Setter for the field updateTimeStamp.

setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Experiment

setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Ius

setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Lane

setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Processing

setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Sample

setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.SequencerRun

setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareExperiment

setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareFile

setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareLane

setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareProcessing

setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareSample

setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareStudy

setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Study

setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Workflow

setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareExperiment

Setter for the field updateTstmp.

setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareFile

Setter for the field updateTstmp.

setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareLane

Setter for the field updateTstmp.

setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareProcessing

Setter for the field updateTstmp.

setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareSample

Setter for the field updateTstmp.

setUpdateValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Setter for the field updateValidator.

setUpdateValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

setUpdateValidator.

setupDirectory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

to be Overridden by the workflow author

setupEnvironment() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

to be Overridden by the workflow author generally people don't override this.

setupFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

to be Overridden by the workflow author the place to specify inputs and outputs to the program also, a user can specify inputs and outputs on jobs directly in which case they are still provisioned properly with respect to the job (inputs before, outputs after) when you define inputs/outputs here they are provisioned before all jobs and after all jobs respectively

setupWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

to be Overridden by the workflow author you generally don't call this as the workflow author since it promotes hardcoding this will typically be filled in by maven

setUrl(String) - Method in class io.seqware.webservice.generated.model.ExperimentLink

setUrl(String) - Method in class io.seqware.webservice.generated.model.File

setUrl(String) - Method in class io.seqware.webservice.generated.model.IusLink

setUrl(String) - Method in class io.seqware.webservice.generated.model.LaneLink

setUrl(String) - Method in class io.seqware.webservice.generated.model.Processing

setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingIus

setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingLanes

setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingSamples

setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingStudies

setUrl(String) - Method in class io.seqware.webservice.generated.model.SampleLink

setUrl(String) - Method in class io.seqware.webservice.generated.model.StudyLink

setUrl(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.common.model.IUSLink

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.common.model.LaneLink

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.common.model.SampleLink

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.common.model.StudyLink

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata

setUrl(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto

Setter for the field url.

setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto

Setter for the field url.

setUrlLabel(String) - Method in class io.seqware.webservice.generated.model.File

setUrlLabel(String) - Method in class io.seqware.webservice.generated.model.Processing

setUrlLabel(String) - Method in class net.sourceforge.seqware.common.model.File

Setter for the field urlLabel.

setUrlLabel(String) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field urlLabel.

setUrlLabel(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata

setUrlLabel(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field urlLabel.

setUseCheckFile(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

setUseIparIntensities(Boolean) - Method in class io.seqware.webservice.generated.model.SequencerRun

setUseIparIntensities(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun

Setter for the field useIparIntensities.

setUseIparIntensities(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

Setter for the field useIparIntensities.

setUseOneURL(Boolean) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field useOneURL.

setUserMl(boolean) - Method in class io.seqware.webservice.generated.model.Registration

setUsername(String) - Method in class io.seqware.webservice.generated.model.Workflow

setUsername(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setUsername(String) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field username.

setUserName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field userName.

setUseTwoURL(Boolean) - Method in class net.sourceforge.seqware.common.model.UploadSequence

Setter for the field useTwoURL.

setUseURL(Boolean) - Method in class net.sourceforge.seqware.common.business.UploadFile

Setter for the field useURL.

setValidationReportService(ValidationReportService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field validationReportService.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController

Setter for the field validator.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.FileController

Setter for the field validator.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController

Setter for the field validator.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController

Setter for the field validator.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController

Setter for the field validator.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController

Setter for the field validator.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController

Setter for the field validator.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO

Setter for the field validator.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController

setValidator.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController

Setter for the field validator.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Setter for the field validator.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController

Setter for the field validator.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController

Setter for the field validator.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController

Setter for the field validator.

setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController

Setter for the field validator.

setValue(String) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute

setValue(String) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute

setValue(String) - Method in class io.seqware.webservice.generated.model.FileAttribute

setValue(String) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute

setValue(String) - Method in class io.seqware.webservice.generated.model.IusAttribute

setValue(String) - Method in class io.seqware.webservice.generated.model.LaneAttribute

setValue(String) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute

setValue(String) - Method in class io.seqware.webservice.generated.model.SampleAttribute

setValue(String) - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute

setValue(String) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute

setValue(String) - Method in class io.seqware.webservice.generated.model.StudyAttribute

setValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute

setValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowParamValue

setValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute

setValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

setValue(String) - Method in interface net.sourceforge.seqware.common.model.Attribute

setValue.

setValue(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute

Setter for the field value.

setValue(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute

setValue.

setValue(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute

setValue.

setValue(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute

Setter for the field value.

setValue(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute

setValue.

setValue(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute

setValue.

setValue(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute

setValue.

setValue(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

setValue.

setValue(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute

setValue.

setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute

setValue.

setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Setter for the field value.

setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

Setter for the field value.

setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute

setValue.

setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

Setter for the field value.

setValue(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit

setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument

Setter for the field value.

setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile

Setter for the field value.

setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement

setValue(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto

Setter for the field value.

setValues(SortedSet<WorkflowParamValue>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Setter for the field values.

setVerbose(boolean) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil

Enable class verbose mode.

setVerbose(boolean) - Static method in class net.sourceforge.seqware.common.util.Log

override the log4j.properties

setVersion(String) - Method in class io.seqware.webservice.generated.model.Processing

setVersion(String) - Method in class io.seqware.webservice.generated.model.Workflow

setVersion(String) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field version.

setVersion(String) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field version.

setVersion(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue

Setter for the field version.

setVersion(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field version.

setVersion(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

set workflow version

setVersion(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

setVisibleParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.solexatools.util.SummaryData

Setter for the field visibleParams.

setWait(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

wait for the workflow to finished, user can override this by using --wait from command line

setWebResource(WebResource) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient

setWfRuns(WorkflowRun[]) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Setter for the field wfRuns.

setWidth(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel

setWithHasFile(SortedSet<Experiment>) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

setWithHasFile.

setWithHasFile(Set<File>, String) - Method in interface net.sourceforge.seqware.common.business.FileService

setWithHasFile.

setWithHasFile(SortedSet<Experiment>) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

setWithHasFile.

setWithHasFile(Set<File>, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

setWithHasFile.

setWithHasFile(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

setWithHasFile.

setWithHasFile(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

setWithHasFile.

setWithHasFile(Set<Processing>) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

setWithHasFile.

setWithHasFile(Set<Processing>, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

setWithHasFile.

setWithHasFile(Integer, SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

setWithHasFile.

setWithHasFile(SortedSet<IUS>) - Method in interface net.sourceforge.seqware.common.business.IUSService

setWithHasFile.

setWithHasFile(SortedSet<Lane>) - Method in interface net.sourceforge.seqware.common.business.LaneService

setWithHasFile.

setWithHasFile(Set<Processing>) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

setWithHasFile.

setWithHasFile(Set<Processing>, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

setWithHasFile.

setWithHasFile(Integer, SortedSet<Sample>) - Method in interface net.sourceforge.seqware.common.business.SampleService

setWithHasFile.

setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.SampleReportRow

Setter for the field workflow.

setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute

Setter for the field workflow.

setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Setter for the field workflow.

setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field workflow.

setWorkflow_engine(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

default is pegasus

setWorkflowAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

setWorkflowAccession(int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field workflowAccession.

setWorkflowAccession(String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

setWorkflowAccessionsToCheck(Set<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

setWorkflowAttributeCollection(Collection<WorkflowAttribute>) - Method in class io.seqware.webservice.generated.model.Workflow

setWorkflowAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute

setWorkflowAttributes(Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field workflowAttributes.

setWorkflowBundleDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

setWorkflowBundleDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow

set the workflowBundle directory

setWorkflowClass(String) - Method in class io.seqware.webservice.generated.model.Workflow

setWorkflowClass(String) - Method in class net.sourceforge.seqware.common.model.Workflow

setWorkflowClass(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

setWorkflowCollection(Collection<Workflow>) - Method in class io.seqware.webservice.generated.model.Registration

setWorkflowDAO(WorkflowDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

setWorkflowDAO.

setWorkflowDAO(WorkflowDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

setWorkflowDAO.

setWorkflowDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

Setter for the field workflowDir.

setWorkflowEngine(String) - Method in class io.seqware.webservice.generated.model.Workflow

setWorkflowEngine(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setWorkflowEngine(String) - Method in class net.sourceforge.seqware.common.model.Workflow

setWorkflowEngine(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

setWorkflowEngine(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

setWorkflowId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport

setWorkflowId(Integer) - Method in class io.seqware.webservice.generated.model.Workflow

setWorkflowId(Workflow) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute

setWorkflowId(Workflow) - Method in class io.seqware.webservice.generated.model.WorkflowParam

setWorkflowId(Workflow) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setWorkflowId(Integer) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field workflowId.

setWorkflowParam(WorkflowParam) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

Setter for the field workflowParam.

setWorkflowParamCollection(Collection<WorkflowParam>) - Method in class io.seqware.webservice.generated.model.Workflow

setWorkflowParamDAO(WorkflowParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl

setWorkflowParamDAO.

setWorkflowParamDAO(WorkflowParamDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService

setWorkflowParamDAO.

setWorkflowParamId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowParam

setWorkflowParamId(WorkflowParam) - Method in class io.seqware.webservice.generated.model.WorkflowParamValue

setWorkflowParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParam

Setter for the field workflowParamId.

setWorkflowParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

Setter for the field workflowParamId.

setWorkflowParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field workflowParams.

setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field workflowParamService.

setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController

Setter for the field workflowParamService.

setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController

Setter for the field workflowParamService.

setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController

Setter for the field workflowParamService.

setWorkflowParamValueCollection(Collection<WorkflowParamValue>) - Method in class io.seqware.webservice.generated.model.WorkflowParam

setWorkflowParamValueDAO(WorkflowParamValueDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl

setWorkflowParamValueDAO.

setWorkflowParamValueDAO(WorkflowParamValueDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService

setWorkflowParamValueDAO.

setWorkflowParamValueId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowParamValue

setWorkflowParamValueId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

Setter for the field workflowParamValueId.

setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field workflowParamValueService.

setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController

Setter for the field workflowParamValueService.

setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController

Setter for the field workflowParamValueService.

setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Setter for the field workflowRun.

setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Expense

Setter for the field workflowRun.

setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field workflowRun.

setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute

Setter for the field workflowRun.

setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

Setter for the field workflowRun.

setWorkflowRun(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setWorkflowRun.

setWorkflowRunAccession(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

setWorkflowRunAccession(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

setWorkflowRunAncesstor(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

setWorkflowRunAncesstor(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

setWorkflowRunAttributeCollection(Collection<WorkflowRunAttribute>) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setWorkflowRunAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute

setWorkflowRunAttributes(Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field workflowRunAttributes.

setWorkflowRunByAncestorWorkflowRunId(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field workflowRunByAncestorWorkflowRunId.

setWorkflowRunCollection(Collection<WorkflowRun>) - Method in class io.seqware.webservice.generated.model.File

setWorkflowRunCollection(Collection<WorkflowRun>) - Method in class io.seqware.webservice.generated.model.Registration

setWorkflowRunCollection(Collection<WorkflowRun>) - Method in class io.seqware.webservice.generated.model.Workflow

setWorkflowRunDAO(WorkflowRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

setWorkflowRunDAO.

setWorkflowRunDAO(WorkflowRunDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

setWorkflowRunDAO.

setWorkflowRunId(Integer) - Method in class io.seqware.webservice.generated.model.Expense

setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns

setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns

setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.Processing

setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

setWorkflowRunId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute

setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.Processing

Setter for the field workflowRunId.

setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

Setter for the field workflowRunId.

setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field workflowRunId.

setWorkflowRunParamCollection(Collection<WorkflowRunParam>) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl

setWorkflowRunParamDAO.

setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

Setter for the field workflowRunParamDAO.

setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService

setWorkflowRunParamDAO.

setWorkflowRunParamId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

setWorkflowRunParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

setWorkflowRunParamId.

setWorkflowRunParams(SortedSet<WorkflowRunParam>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun

Setter for the field workflowRunParams.

setWorkflowRunProcessings(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

Setter for the field workflowRunProcessings.

setWorkflowRunRunning(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setWorkflowRunRunning.

setWorkflowRunRunningWithSample(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setWorkflowRunRunningWithSample.

setWorkflowRuns(Set<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.IUS

Setter for the field workflowRuns.

setWorkflowRuns(Set<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.Lane

Setter for the field workflowRuns.

setWorkflowRuns(SortedSet<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.Workflow

Setter for the field workflowRuns.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.RetryAnalysisWorkflowController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController

Setter for the field workflowRunService.

setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController

Setter for the field workflowRunService.

setWorkflowRunWithSample(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession

setWorkflowRunWithSample.

setWorkflows(ArrayList<WorkflowInfo>) - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo

Setter for the field workflows.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.seqware.common.ContextImpl

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController

Setter for the field workflowService.

setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController

Setter for the field workflowService.

setWorkflowSqwVersion(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

setWorkflowSqwVersion.

setWorkflowTemplate(String) - Method in class io.seqware.webservice.generated.model.Workflow

setWorkflowTemplate(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun

setWorkflowType(String) - Method in class io.seqware.webservice.generated.model.Workflow

setWorkflowType(String) - Method in class net.sourceforge.seqware.common.model.Workflow

setWorkflowType(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

setWorkflowType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

Set the value of workflowType

SGE_MAX_MEMORY_PARAM_VARIABLE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

Variable identifier to be used within the qsub max-memory parameter to specify the value.

SGE_THREADS_PARAM_VARIABLE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

Variable identifier to be used within the qsub threads parameter to specify the value.

SGE_XMLNS - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

Namespace of the Oozie SGE action xml node.

ShareExperiment - Class in io.seqware.webservice.generated.model

ShareExperiment() - Constructor for class io.seqware.webservice.generated.model.ShareExperiment

ShareExperiment(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareExperiment

ShareExperiment(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareExperiment

ShareExperiment - Class in net.sourceforge.seqware.common.model

ShareExperiment generated by hbm2java

ShareExperiment() - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment

Constructor for ShareExperiment.

ShareExperiment(int, Experiment, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment

Constructor for ShareExperiment.

ShareExperiment(int, Experiment, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment

Constructor for ShareExperiment.

ShareExperimentDAO - Interface in net.sourceforge.seqware.common.dao

ShareExperimentDAO interface.

ShareExperimentDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ShareExperimentDAOHibernate class.

ShareExperimentDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate

ShareExperimentFacadeREST - Class in io.seqware.webservice.generated.controller

ShareExperimentFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareExperimentFacadeREST

ShareExperimentService - Interface in net.sourceforge.seqware.common.business

ShareExperimentService interface.

ShareExperimentServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ShareExperimentServiceImpl class.

ShareExperimentServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl

ShareFile - Class in io.seqware.webservice.generated.model

ShareFile() - Constructor for class io.seqware.webservice.generated.model.ShareFile

ShareFile(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareFile

ShareFile(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareFile

ShareFile - Class in net.sourceforge.seqware.common.model

ShareFile generated by hbm2java

ShareFile() - Constructor for class net.sourceforge.seqware.common.model.ShareFile

Constructor for ShareFile.

ShareFile(int, File, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareFile

Constructor for ShareFile.

ShareFile(int, File, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareFile

Constructor for ShareFile.

ShareFileDAO - Interface in net.sourceforge.seqware.common.dao

ShareFileDAO interface.

ShareFileDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ShareFileDAOHibernate class.

ShareFileDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate

ShareFileFacadeREST - Class in io.seqware.webservice.generated.controller

ShareFileFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareFileFacadeREST

ShareFileService - Interface in net.sourceforge.seqware.common.business

ShareFileService interface.

ShareFileServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ShareFileServiceImpl class.

ShareFileServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl

ShareLane - Class in io.seqware.webservice.generated.model

ShareLane() - Constructor for class io.seqware.webservice.generated.model.ShareLane

ShareLane(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareLane

ShareLane(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareLane

ShareLane - Class in net.sourceforge.seqware.common.model

ShareLane generated by hbm2java

ShareLane() - Constructor for class net.sourceforge.seqware.common.model.ShareLane

Constructor for ShareLane.

ShareLane(int, Lane, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareLane

Constructor for ShareLane.

ShareLane(int, Lane, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareLane

Constructor for ShareLane.

ShareLaneDAO - Interface in net.sourceforge.seqware.common.dao

ShareLaneDAO interface.

ShareLaneDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ShareLaneDAOHibernate class.

ShareLaneDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate

ShareLaneFacadeREST - Class in io.seqware.webservice.generated.controller

ShareLaneFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareLaneFacadeREST

ShareLaneService - Interface in net.sourceforge.seqware.common.business

ShareLaneService interface.

ShareLaneServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ShareLaneServiceImpl class.

ShareLaneServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl

ShareProcessing - Class in io.seqware.webservice.generated.model

ShareProcessing() - Constructor for class io.seqware.webservice.generated.model.ShareProcessing

ShareProcessing(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareProcessing

ShareProcessing(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareProcessing

ShareProcessing - Class in net.sourceforge.seqware.common.model

ShareProcessing generated by hbm2java

ShareProcessing() - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing

Constructor for ShareProcessing.

ShareProcessing(int, Processing, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing

Constructor for ShareProcessing.

ShareProcessing(int, Processing, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing

Constructor for ShareProcessing.

ShareProcessingDAO - Interface in net.sourceforge.seqware.common.dao

ShareProcessingDAO interface.

ShareProcessingDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ShareProcessingDAOHibernate class.

ShareProcessingDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate

ShareProcessingFacadeREST - Class in io.seqware.webservice.generated.controller

ShareProcessingFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareProcessingFacadeREST

ShareProcessingService - Interface in net.sourceforge.seqware.common.business

ShareProcessingService interface.

ShareProcessingServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ShareProcessingServiceImpl class.

ShareProcessingServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl

ShareSample - Class in io.seqware.webservice.generated.model

ShareSample() - Constructor for class io.seqware.webservice.generated.model.ShareSample

ShareSample(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareSample

ShareSample(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareSample

ShareSample - Class in net.sourceforge.seqware.common.model

ShareSample generated by hbm2java

ShareSample() - Constructor for class net.sourceforge.seqware.common.model.ShareSample

Constructor for ShareSample.

ShareSample(int, Sample, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareSample

Constructor for ShareSample.

ShareSample(int, Sample, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareSample

Constructor for ShareSample.

ShareSampleDAO - Interface in net.sourceforge.seqware.common.dao

ShareSampleDAO interface.

ShareSampleDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ShareSampleDAOHibernate class.

ShareSampleDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate

ShareSampleFacadeREST - Class in io.seqware.webservice.generated.controller

ShareSampleFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareSampleFacadeREST

ShareSampleService - Interface in net.sourceforge.seqware.common.business

ShareSampleService interface.

ShareSampleServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ShareSampleServiceImpl class.

ShareSampleServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl

ShareStudy - Class in io.seqware.webservice.generated.model

ShareStudy() - Constructor for class io.seqware.webservice.generated.model.ShareStudy

ShareStudy(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareStudy

ShareStudy(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareStudy

ShareStudy - Class in net.sourceforge.seqware.common.model

ShareStudy class.

ShareStudy() - Constructor for class net.sourceforge.seqware.common.model.ShareStudy

Constructor for ShareStudy.

ShareStudyDAO - Interface in net.sourceforge.seqware.common.dao

ShareStudyDAO interface.

ShareStudyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ShareStudyDAOHibernate class.

ShareStudyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate

Constructor for ShareStudyDAOHibernate.

ShareStudyFacadeREST - Class in io.seqware.webservice.generated.controller

ShareStudyFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareStudyFacadeREST

ShareStudyService - Interface in net.sourceforge.seqware.common.business

ShareStudyService interface.

ShareStudyServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ShareStudyServiceImpl class.

ShareStudyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl

Constructor for ShareStudyServiceImpl.

ShareValidatorController - Class in net.sourceforge.solexatools.webapp.controller

ShareValidatorController class.

ShareValidatorController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ShareValidatorController

Constructor for ShareValidatorController.

ShareWorkflowRun - Class in io.seqware.webservice.generated.model

ShareWorkflowRun() - Constructor for class io.seqware.webservice.generated.model.ShareWorkflowRun

ShareWorkflowRun(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareWorkflowRun

ShareWorkflowRun(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareWorkflowRun

ShareWorkflowRun - Class in net.sourceforge.seqware.common.model

ShareWorkflowRun class.

ShareWorkflowRun() - Constructor for class net.sourceforge.seqware.common.model.ShareWorkflowRun

Constructor for ShareWorkflowRun.

ShareWorkflowRunDAO - Interface in net.sourceforge.seqware.common.dao

ShareWorkflowRunDAO interface.

ShareWorkflowRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

ShareWorkflowRunDAOHibernate class.

ShareWorkflowRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate

Constructor for ShareWorkflowRunDAOHibernate.

ShareWorkflowRunFacadeREST - Class in io.seqware.webservice.generated.controller

ShareWorkflowRunFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareWorkflowRunFacadeREST

ShareWorkflowRunService - Interface in net.sourceforge.seqware.common.business

ShareWorkflowRunService interface.

ShareWorkflowRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ShareWorkflowRunServiceImpl class.

ShareWorkflowRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl

Constructor for ShareWorkflowRunServiceImpl.

SHOW_STATUS - Static variable in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter

SignUpController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp

SignUpController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SignUpController

Constructor for SignUpController.

SimpleFileLock - Class in net.sourceforge.seqware.common.util.filetools.lock

Deprecated.

SimpleFileLock(String) - Constructor for class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock

Deprecated.

Constructor for SimpleFileLock.

SimpleFileLock(File) - Constructor for class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock

Deprecated.

Constructor for SimpleFileLock.

size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs

size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles

size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles

SIZE_COUNT_FILE - Static variable in class net.sourceforge.solexatools.util.PaginationUtil

Constant SIZE_COUNT_FILE=5

SIZE_COUNT_TREE - Static variable in class net.sourceforge.solexatools.util.PaginationUtil

Constant SIZE_COUNT_TREE=20

sleep(int) - Static method in class net.sourceforge.seqware.common.util.processtools.ProcessTools

sleep.

someString() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryResource

someString.

SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant SORT_NAME="sortname"

SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController

Constant SORT_NAME="sortname"

SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant SORT_NAME="sortname"

SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant SORT_ORDER="sortorder"

SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController

Constant SORT_ORDER="sortorder"

SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant SORT_ORDER="sortorder"

SORT_ORDER_ASC - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant SORT_ORDER_ASC="asc"

SORT_ORDER_ASC - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant SORT_ORDER_ASC="asc"

SORT_ORDER_DESC - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant SORT_ORDER_DESC="desc"

SORT_ORDER_DESC - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant SORT_ORDER_DESC="desc"

spaceSeparateMy(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider

splitFile(File, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

splitFile.

SQLQUERYFAILED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant SQLQUERYFAILED=82

SqwFile - Class in net.sourceforge.seqware.pipeline.workflowV2.model

a file object which has all information for provision

SqwFile() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile

stackTraceToString(Throwable) - Static method in class net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools

stackTraceToString.

standard - Variable in enum net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility.HumanProvenanceFilters

startCommand(Map<String, String>, String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools

startCommand.

startCommand(String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools

startCommand.

startCommand(String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools

startCommand.

startCommand(Map<String, String>, String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools

An alternate runner that launches a process and returns it so that the caller can process it's output directly.

status - Variable in exception net.sourceforge.seqware.common.util.ExitException

statusCounts - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools

stderr - Variable in class net.sourceforge.seqware.common.module.ReturnValue

stderr(String) - Static method in class net.sourceforge.seqware.common.util.Log

stderr.

StdErr - Class in net.sourceforge.seqware.common.util.processtools.stderr

StdErr class.

StdErr() - Constructor for class net.sourceforge.seqware.common.util.processtools.stderr.StdErr

stderr2string(Process) - Static method in class net.sourceforge.seqware.common.util.processtools.stderr.StdErr

stderr2string.

StderrRedirect - Annotation Type in net.sourceforge.seqware.pipeline.module

Annotation type to tag where to start Stderr redirect Created by IntelliJ IDEA.

stdout - Variable in class net.sourceforge.seqware.common.module.ReturnValue

stdout(String) - Static method in class net.sourceforge.seqware.common.util.Log

stdout.

StdOut - Class in net.sourceforge.seqware.common.util.processtools.stdout

StdOut class.

StdOut() - Constructor for class net.sourceforge.seqware.common.util.processtools.stdout.StdOut

stdout2file(Process, File, boolean) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut

stdout2file.

stdout2file(Process, ArrayList<File>, boolean, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut

stdout2file.

stdout2fileBinary(Process, File) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut

stdout2fileBinary.

stdout2fileBinary(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut

stdout2fileBinary.

stdout2fileEncoded(Process, File) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut

stdout2fileEncoded.

stdout2fileEncoded(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut

stdout2fileEncoded.

stdout2fileEncodedStripQualPrimer(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut

stdout2fileEncodedStripQualPrimer.

STDOUTERR - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant STDOUTERR=90

StdoutRedirect - Annotation Type in net.sourceforge.seqware.pipeline.module

Interface for declaring when to do the Created by IntelliJ IDEA.

stdoutWithTime(String) - Static method in class net.sourceforge.seqware.common.util.Log

Output to stdout with the time pre-pended

stop() - Static method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceMain

stop.

Str - Class in net.sourceforge.seqware.common.util

Str() - Constructor for class net.sourceforge.seqware.common.util.Str

Str.UnsafeName - Exception in net.sourceforge.seqware.common.util

Str.UnsafeName(String) - Constructor for exception net.sourceforge.seqware.common.util.Str.UnsafeName

StringUtils - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus

StringUtils class.

StringUtils() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.StringUtils

stripInvalidXmlCharacters(String) - Static method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker

Stolen from https://stackoverflow.com/questions/93655/stripping-invalid-xml-characters-in-java/9635310#9635310

Studies - Class in io.seqware

Studies() - Constructor for class io.seqware.Studies

studiesTsv() - Static method in class io.seqware.Studies

Study - Class in io.seqware.webservice.generated.model

Study() - Constructor for class io.seqware.webservice.generated.model.Study

Study(Integer) - Constructor for class io.seqware.webservice.generated.model.Study

Study(Integer, String, String, String, int, Date) - Constructor for class io.seqware.webservice.generated.model.Study

Study - Class in net.sourceforge.seqware.common.model

Study() - Constructor for class net.sourceforge.seqware.common.model.Study

Constructor for Study.

STUDY_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant STUDY_ATTRIBUTES="Header.STUDY_ATTRIBUTES.getTitle()"

STUDY_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController

Constant STUDY_ID="study_id"

STUDY_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant STUDY_ID="study_id"

STUDY_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant

Constant STUDY_PREFIX="study_"

STUDY_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant STUDY_SWA="Header.STUDY_SWA.getTitle()"

STUDY_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant STUDY_TAG_PREFIX="Header.STUDY_TAG_PREFIX.getTitle()"

STUDY_TITLE - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant STUDY_TITLE="Header.STUDY_TITLE.getTitle()"

STUDY_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant

Constant STUDY_VIEW="redirect:/myStudyList.htm"

StudyAttribute - Class in io.seqware.webservice.generated.model

StudyAttribute() - Constructor for class io.seqware.webservice.generated.model.StudyAttribute

StudyAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.StudyAttribute

StudyAttribute(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.StudyAttribute

StudyAttribute - Class in net.sourceforge.seqware.common.model

StudyAttribute generated by hbm2java

StudyAttribute() - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute

Constructor for StudyAttribute.

StudyAttribute(int, Study, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute

Constructor for StudyAttribute.

StudyAttribute(int, Study, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute

Constructor for StudyAttribute.

StudyAttributeDAO - Interface in net.sourceforge.seqware.common.dao

StudyAttributeDAO interface.

StudyAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

StudyAttributeDAOHibernate class.

StudyAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate

StudyAttributeFacadeREST - Class in io.seqware.webservice.generated.controller

StudyAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.StudyAttributeFacadeREST

StudyBuildTree - Class in net.sourceforge.solexatools.util

StudyBuildTree class.

StudyBuildTree() - Constructor for class net.sourceforge.solexatools.util.StudyBuildTree

StudyController - Class in net.sourceforge.solexatools.webapp.controller

StudyController

StudyController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyController

Constructor for StudyController.

StudyController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyController

Constructor for StudyController.

StudyDAO - Interface in net.sourceforge.seqware.common.dao

StudyDAO interface.

StudyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

StudyDAOHibernate class.

StudyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

Constructor for StudyDAOHibernate.

StudyFacadeREST - Class in io.seqware.webservice.generated.controller

StudyFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.StudyFacadeREST

StudyHtmlUtil - Class in net.sourceforge.solexatools.util

StudyHtmlUtil class.

StudyHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.StudyHtmlUtil

StudyIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries

StudyIdFilesResource class.

StudyIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesResource

Constructor for StudyIdFilesResource.

StudyIdFilesTSVResource - Class in net.sourceforge.seqware.webservice.resources.queries

StudyIdFilesTSVResource class.

StudyIdFilesTSVResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesTSVResource

Constructor for StudyIdFilesTSVResource.

StudyIDResource - Class in net.sourceforge.seqware.webservice.resources.tables

StudyIDResource class.

StudyIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource

Constructor for StudyIDResource.

StudyLink - Class in io.seqware.webservice.generated.model

StudyLink() - Constructor for class io.seqware.webservice.generated.model.StudyLink

StudyLink(Integer) - Constructor for class io.seqware.webservice.generated.model.StudyLink

StudyLink(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.StudyLink

StudyLink - Class in net.sourceforge.seqware.common.model

StudyLink generated by hbm2java

StudyLink() - Constructor for class net.sourceforge.seqware.common.model.StudyLink

Constructor for StudyLink.

StudyLink(int, Study, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyLink

Constructor for StudyLink.

StudyLink(int, Study, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyLink

Constructor for StudyLink.

StudyLinkDAO - Interface in net.sourceforge.seqware.common.dao

StudyLinkDAO interface.

StudyLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

StudyLinkDAOHibernate class.

StudyLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate

StudyLinkFacadeREST - Class in io.seqware.webservice.generated.controller

StudyLinkFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.StudyLinkFacadeREST

StudyList - Class in net.sourceforge.seqware.common.model.lists

StudyList class.

StudyList() - Constructor for class net.sourceforge.seqware.common.model.lists.StudyList

Constructor for StudyList.

StudyListController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController

StudyListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListController

Constructor for StudyListController.

StudyListDetailsController - Class in net.sourceforge.solexatools.webapp.controller

StudyListDetailsController class.

StudyListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController

Constructor for StudyListDetailsController.

StudyListDetailsFlatController - Class in net.sourceforge.solexatools.webapp.controller

StudyListDetailsFlatController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController

StudyReportBoxController - Class in net.sourceforge.solexatools.webapp.controller

StudyReportBoxController class.

StudyReportBoxController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController

StudyReportController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController

StudyReportController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportController

Constructor for StudyReportController.

StudyReportSetupController - Class in net.sourceforge.solexatools.webapp.controller

StudyReportSetupController class.

StudyReportSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController

StudyReportTableController - Class in net.sourceforge.solexatools.webapp.controller

StudyReportTableController class.

StudyReportTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constructor for StudyReportTableController.

StudyResource - Class in net.sourceforge.seqware.webservice.resources.tables

StudyResource class.

StudyResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyResource

Constructor for StudyResource.

StudySampleReportFileLineItem - Class in net.sourceforge.solexatools.webapp.metamodel

StudySampleReportFileLineItem class.

StudySampleReportFileLineItem(Sample, Sample, IUS, File) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem

Constructor for StudySampleReportFileLineItem.

StudySampleReportLineItem - Class in net.sourceforge.solexatools.webapp.metamodel

StudySampleReportLineItem class.

StudySampleReportLineItem(Sample, Sample, String[]) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem

Constructor for StudySampleReportLineItem.

StudyService - Interface in net.sourceforge.seqware.common.business

StudyService interface.

StudyServiceImpl - Class in net.sourceforge.seqware.common.business.impl

StudyServiceImpl class.

StudyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

Constructor for StudyServiceImpl.

StudySetupController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController

StudySetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudySetupController

Constructor for StudySetupController.

StudyTableController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController

StudyTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyTableController

Constructor for AnalisysListController.

StudyTableControllerDetails - Class in net.sourceforge.solexatools.webapp.controller

TODO: * it would be best if this controller would actually render the workflow_runs too.

StudyTableControllerDetails() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyTableControllerDetails

Constructor for AnalisysListController.

StudyType - Class in io.seqware.webservice.generated.model

StudyType() - Constructor for class io.seqware.webservice.generated.model.StudyType

StudyType(Integer) - Constructor for class io.seqware.webservice.generated.model.StudyType

StudyType(Integer, String) - Constructor for class io.seqware.webservice.generated.model.StudyType

StudyType - Class in net.sourceforge.seqware.common.model

StudyType class.

StudyType() - Constructor for class net.sourceforge.seqware.common.model.StudyType

StudyTypeDAO - Interface in net.sourceforge.seqware.common.dao

StudyTypeDAO interface.

StudyTypeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

StudyTypeDAOHibernate class.

StudyTypeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate

Constructor for StudyTypeDAOHibernate.

StudyTypeFacadeREST - Class in io.seqware.webservice.generated.controller

StudyTypeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.StudyTypeFacadeREST

StudyTypeList - Class in net.sourceforge.seqware.common.model.lists

StudyTypeList class.

StudyTypeList() - Constructor for class net.sourceforge.seqware.common.model.lists.StudyTypeList

Constructor for StudyTypeList.

StudyTypeResource - Class in net.sourceforge.seqware.webservice.resources.tables

ExperimentResource class.

StudyTypeResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyTypeResource

Constructor for ExperimentResource.

StudyTypeService - Interface in net.sourceforge.seqware.common.business

StudyTypeService interface.

StudyTypeServiceImpl - Class in net.sourceforge.seqware.common.business.impl

StudyTypeServiceImpl class.

StudyTypeServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl

Constructor for StudyTypeServiceImpl.

StudyUpdateValidator - Class in net.sourceforge.solexatools.validation

StudyUpdateValidator() - Constructor for class net.sourceforge.solexatools.validation.StudyUpdateValidator

StudyValidator - Class in net.sourceforge.solexatools.validation

StudyValidator class.

StudyValidator() - Constructor for class net.sourceforge.solexatools.validation.StudyValidator

Constructor for StudyValidator.

subList(int, int, List) - Static method in class net.sourceforge.solexatools.util.PaginationUtil

subList.

subList(HttpServletRequest, String, List<T>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil

subList.

subList(HttpServletRequest, String, int, List<T>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil

subList.

subListSD(HttpServletRequest, String, List) - Static method in class net.sourceforge.solexatools.util.PaginationUtil

subListSD.

submitCancel(int) - Static method in class io.seqware.WorkflowRuns

submitRetry(int) - Static method in class io.seqware.WorkflowRuns

SUCCESS - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant SUCCESS=0

SummaryData - Class in net.sourceforge.solexatools.util

SummaryData class.

SummaryData() - Constructor for class net.sourceforge.solexatools.util.SummaryData

Constructor for SummaryData.

SummaryLaunchWorkflowController - Class in net.sourceforge.solexatools.webapp.controller

SummaryLaunchWorkflowController class.

SummaryLaunchWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController

Constructor for SummaryLaunchWorkflowController.

SummaryLaunchWorkflowController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController

Constructor for SummaryLaunchWorkflowController.

SummaryLine - Class in net.sourceforge.solexatools.util

SummaryLine class.

SummaryLine() - Constructor for class net.sourceforge.solexatools.util.SummaryLine

Constructor for SummaryLine.

supports(Class) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator

supports(Class) - Method in class net.sourceforge.solexatools.validation.LaneValidator

supports(Class) - Method in class net.sourceforge.solexatools.validation.LoginValidator

Returns true if this Validator supports the specified Class, and false otherwise.

supports(Class) - Method in class net.sourceforge.solexatools.validation.SampleValidator

supports(Class) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator

supports(Class) - Method in class net.sourceforge.solexatools.validation.SequencerRunWizardValidator

supports(Class) - Method in class net.sourceforge.solexatools.validation.StudyValidator

supports(Class) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator

supports(Class) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator

supports(Class) - Method in class net.sourceforge.solexatools.validation.WorkflowParamValidator

supports(Class) - Method in class net.sourceforge.solexatools.validation.WorkflowValidator

supportsCancel(String) - Static method in class io.seqware.Engines

supportsRetry(String) - Static method in class io.seqware.Engines

SwBadFileException - Exception in net.sourceforge.seqware.common.err

Created by IntelliJ IDEA.

SwBadFileException() - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException

Constructor for SwBadFileException.

SwBadFileException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException

Constructor for SwBadFileException.

SwBadFileException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException

Constructor for SwBadFileException.

SwBadFileException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException

Constructor for SwBadFileException.

SwBadModuleException - Exception in net.sourceforge.seqware.common.err

User: Xiaoshu Wang (xiao@renci.org) Date: 9/1/11 Time: 2:56 PM

SwBadModuleException() - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException

Constructor for SwBadModuleException.

SwBadModuleException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException

Constructor for SwBadModuleException.

SwBadModuleException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException

Constructor for SwBadModuleException.

SwBadModuleException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException

Constructor for SwBadModuleException.

SwParameterException - Exception in net.sourceforge.seqware.common.err

Created by IntelliJ IDEA.

SwParameterException() - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException

Constructor for SwParameterException.

SwParameterException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException

Constructor for SwParameterException.

SwParameterException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException

Constructor for SwParameterException.

SwParameterException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException

Constructor for SwParameterException.

SwRunnerParameterException - Exception in net.sourceforge.seqware.common.err

User: Xiaoshu Wang (xiao@renci.org) Date: 9/6/11 Time: 3:20 PM

SwRunnerParameterException() - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException

Constructor for SwRunnerParameterException.

SwRunnerParameterException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException

Constructor for SwRunnerParameterException.

SwRunnerParameterException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException

Constructor for SwRunnerParameterException.

SwRunnerParameterException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException

Constructor for SwRunnerParameterException.

symDifference(Set<T>, Set<T>) - Static method in class net.sourceforge.seqware.pipeline.tools.SetOperations

SymLinkFileReporter - Class in net.sourceforge.seqware.pipeline.plugins

SymLinkFileReporter class.

SymLinkFileReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter

Constructor for SymLinkFileReporter.

T

TabExpansionUtil - Class in net.sourceforge.seqware.common.util

A series of utility methods that produce human friendly output from tabbed output.

TabExpansionUtil() - Constructor for class net.sourceforge.seqware.common.util.TabExpansionUtil

table - Variable in class net.sourceforge.seqware.webservice.resources.tables.DatabaseResource

TABLE_MODEL - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant TABLE_MODEL="tablemodel"

TABLE_MODEL - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant TABLE_MODEL="tablemodel"

TABLE_SEL - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController

Constant TABLE_SEL="tablesel"

TABLE_SEL - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController

Constant TABLE_SEL="tablesel"

TagUtils - Class in net.sourceforge.solexatools.util

TagUtils class.

TagUtils() - Constructor for class net.sourceforge.solexatools.util.TagUtils

TagValueUnit - Class in net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection

TagValueUnit() - Constructor for class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit

test(String[]) - Method in class net.sourceforge.seqware.pipeline.tools.ReportTest

test.

testBundle(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

testBundle.

testBundle(File, File, String, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

A bundle test occurs without metadata writeback

TestDatabaseCreator - Class in net.sourceforge.seqware.metadb.util

This class handles basic database creation.

TestDatabaseCreator() - Constructor for class net.sourceforge.seqware.metadb.util.TestDatabaseCreator

testIfNull(Object) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport

testIfNull.

testIfNull(T) - Static method in class net.sourceforge.seqware.webservice.resources.BasicResource

testIfNull.

TestModule - Class in net.sourceforge.seqware.pipeline.module

This is an empty module mainly for testing purpose.

TestModule() - Constructor for class net.sourceforge.seqware.pipeline.module.TestModule

threadsSgeParamFormat - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

THRESHOLD - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp

throwExceptionWithMessage(String) - Static method in class io.seqware.webservice.controller.UtilityREST

TimestampFormatterAdapter - Class in io.seqware.webservice.adapter

Allows for conversion for the Timestamp values backing the @Version columns used for optimistic locking

TimestampFormatterAdapter() - Constructor for class io.seqware.webservice.adapter.TimestampFormatterAdapter

tList - Variable in class net.sourceforge.seqware.common.model.lists.ExperimentLibraryDesignList

tList - Variable in class net.sourceforge.seqware.common.model.lists.ExperimentList

tList - Variable in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignList

tList - Variable in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignReadSpecList

tList - Variable in class net.sourceforge.seqware.common.model.lists.FileList

tList - Variable in class net.sourceforge.seqware.common.model.lists.IntegerList

tList - Variable in class net.sourceforge.seqware.common.model.lists.IUSList

tList - Variable in class net.sourceforge.seqware.common.model.lists.LaneList

tList - Variable in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList

tList - Variable in class net.sourceforge.seqware.common.model.lists.LibrarySourceList

tList - Variable in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList

tList - Variable in class net.sourceforge.seqware.common.model.lists.OrganismList

tList - Variable in class net.sourceforge.seqware.common.model.lists.PlatformList

tList - Variable in class net.sourceforge.seqware.common.model.lists.ProcessingList

tList - Variable in class net.sourceforge.seqware.common.model.lists.ReturnValueList

tList - Variable in class net.sourceforge.seqware.common.model.lists.SampleList

tList - Variable in class net.sourceforge.seqware.common.model.lists.SequencerRunList

tList - Variable in class net.sourceforge.seqware.common.model.lists.StudyList

tList - Variable in class net.sourceforge.seqware.common.model.lists.StudyTypeList

tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowList

tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowParamList

tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList

tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowRunList

tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2

toString() - Method in class io.seqware.webservice.generated.model.Expense

toString() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute

toString() - Method in class io.seqware.webservice.generated.model.Experiment

toString() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute

toString() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign

toString() - Method in class io.seqware.webservice.generated.model.ExperimentLink

toString() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign

toString() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec

toString() - Method in class io.seqware.webservice.generated.model.File

toString() - Method in class io.seqware.webservice.generated.model.FileAttribute

toString() - Method in class io.seqware.webservice.generated.model.FileReport

toString() - Method in class io.seqware.webservice.generated.model.FileType

toString() - Method in class io.seqware.webservice.generated.model.Invoice

toString() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute

toString() - Method in class io.seqware.webservice.generated.model.Ius

toString() - Method in class io.seqware.webservice.generated.model.IusAttribute

toString() - Method in class io.seqware.webservice.generated.model.IusLink

toString() - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns

toString() - Method in class io.seqware.webservice.generated.model.Lane

toString() - Method in class io.seqware.webservice.generated.model.LaneAttribute

toString() - Method in class io.seqware.webservice.generated.model.LaneLink

toString() - Method in class io.seqware.webservice.generated.model.LaneType

toString() - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns

toString() - Method in class io.seqware.webservice.generated.model.LibrarySelection

toString() - Method in class io.seqware.webservice.generated.model.LibrarySource

toString() - Method in class io.seqware.webservice.generated.model.LibraryStrategy

toString() - Method in class io.seqware.webservice.generated.model.Organism

toString() - Method in class io.seqware.webservice.generated.model.Platform

toString() - Method in class io.seqware.webservice.generated.model.Processing

toString() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute

toString() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments

toString() - Method in class io.seqware.webservice.generated.model.ProcessingFiles

toString() - Method in class io.seqware.webservice.generated.model.ProcessingIus

toString() - Method in class io.seqware.webservice.generated.model.ProcessingLanes

toString() - Method in class io.seqware.webservice.generated.model.ProcessingRelationship

toString() - Method in class io.seqware.webservice.generated.model.ProcessingSamples

toString() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns

toString() - Method in class io.seqware.webservice.generated.model.ProcessingStudies

toString() - Method in class io.seqware.webservice.generated.model.Registration

toString() - Method in class io.seqware.webservice.generated.model.Sample

toString() - Method in class io.seqware.webservice.generated.model.SampleAttribute

toString() - Method in class io.seqware.webservice.generated.model.SampleLink

toString() - Method in class io.seqware.webservice.generated.model.SampleRelationship

toString() - Method in class io.seqware.webservice.generated.model.SampleReport

toString() - Method in class io.seqware.webservice.generated.model.SampleSearch

toString() - Method in class io.seqware.webservice.generated.model.SampleSearchAttribute

toString() - Method in class io.seqware.webservice.generated.model.SequencerRun

toString() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute

toString() - Method in class io.seqware.webservice.generated.model.ShareExperiment

toString() - Method in class io.seqware.webservice.generated.model.ShareFile

toString() - Method in class io.seqware.webservice.generated.model.ShareLane

toString() - Method in class io.seqware.webservice.generated.model.ShareProcessing

toString() - Method in class io.seqware.webservice.generated.model.ShareSample

toString() - Method in class io.seqware.webservice.generated.model.ShareStudy

toString() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun

toString() - Method in class io.seqware.webservice.generated.model.Study

toString() - Method in class io.seqware.webservice.generated.model.StudyAttribute

toString() - Method in class io.seqware.webservice.generated.model.StudyLink

toString() - Method in class io.seqware.webservice.generated.model.StudyType

toString() - Method in class io.seqware.webservice.generated.model.Workflow

toString() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute

toString() - Method in class io.seqware.webservice.generated.model.WorkflowParam

toString() - Method in class io.seqware.webservice.generated.model.WorkflowParamValue

toString() - Method in class io.seqware.webservice.generated.model.WorkflowRun

toString() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute

toString() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam

toString() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row

toString() - Method in class net.sourceforge.seqware.common.model.Expense

toString() - Method in class net.sourceforge.seqware.common.model.Experiment

toString() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign

toString.

toString() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign

toString.

toString() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec

toString() - Method in class net.sourceforge.seqware.common.model.File

toString() - Method in enum net.sourceforge.seqware.common.model.FileProvenanceParam

toString() - Method in class net.sourceforge.seqware.common.model.FileType

toString() - Method in class net.sourceforge.seqware.common.model.Invoice

toString() - Method in class net.sourceforge.seqware.common.model.IUS

toString() - Method in class net.sourceforge.seqware.common.model.IUSAttribute

toString() - Method in class net.sourceforge.seqware.common.model.Lane

toString() - Method in class net.sourceforge.seqware.common.model.LaneAttribute

toString() - Method in class net.sourceforge.seqware.common.model.LibrarySelection

toString() - Method in class net.sourceforge.seqware.common.model.LibrarySource

toString() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy

toString() - Method in class net.sourceforge.seqware.common.model.Organism

toString() - Method in class net.sourceforge.seqware.common.model.Platform

toString() - Method in class net.sourceforge.seqware.common.model.Processing

toString() - Method in class net.sourceforge.seqware.common.model.Registration

toString() - Method in class net.sourceforge.seqware.common.model.Sample

toString() - Method in class net.sourceforge.seqware.common.model.SequencerRun

toString() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute

toString() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO

toString() - Method in class net.sourceforge.seqware.common.model.ShareStudy

toString() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun

toString() - Method in class net.sourceforge.seqware.common.model.Study

toString() - Method in class net.sourceforge.seqware.common.model.StudyType

toString() - Method in class net.sourceforge.seqware.common.model.Workflow

toString() - Method in class net.sourceforge.seqware.common.model.WorkflowParam

toString() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue

toString() - Method in class net.sourceforge.seqware.common.model.WorkflowRun

toString() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam

toString.

toString() - Method in class net.sourceforge.seqware.common.module.FileMetadata

toString() - Method in class net.sourceforge.seqware.common.module.ReturnValue

toString() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo

toString() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo

toString() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo

toString() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine

toString() - Method in enum net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility.HumanProvenanceFilters

toString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

toString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command

toString(WorkflowRunReportRow, StringBuilder) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource

toString.

totalSteps - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools

totalSteps - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

trace(Object) - Static method in class net.sourceforge.seqware.common.util.Log

See Category.debug(Object).

trace(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log

See Category.debug(Object,Throwable).

TreeNodeHtmlUtil - Class in net.sourceforge.solexatools.util

TreeNodeHtmlUtil class.

TreeNodeHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.TreeNodeHtmlUtil

TriggerFileProvenanceResource - Class in net.sourceforge.seqware.webservice.resources.queries

TriggerFileProvenanceResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.TriggerFileProvenanceResource

triggerProvenanceReport() - Static method in class io.seqware.Reports

TutorialCheck - Class in io.seqware.pipeline.plugins.sanity.checks

Runs through our pre-CLI tutorial

TutorialCheck() - Constructor for class io.seqware.pipeline.plugins.sanity.checks.TutorialCheck

TYPE_TREE - Static variable in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil

Constant TYPE_TREE="sr"

TYPE_TREE - Static variable in class net.sourceforge.solexatools.util.StudyHtmlUtil

Constant TYPE_TREE="st"

TYPE_TREE_COMPLETED - Static variable in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil

Constant TYPE_TREE_COMPLETED="wfr"

TYPE_TREE_RUNNNING - Static variable in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil

Constant TYPE_TREE_RUNNNING="wfrr"

U

unBindSessionFromTheThread() - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions

unBindSessionFromTheThread.

UNCKerberos - Class in net.sourceforge.solexatools.authentication

UNCKerberos class.

UNCKerberos() - Constructor for class net.sourceforge.solexatools.authentication.UNCKerberos

UNCKerberos.NamePasswordCallbackHandler - Class in net.sourceforge.solexatools.authentication

UNCKerberos.NamePasswordCallbackHandler(String, String) - Constructor for class net.sourceforge.solexatools.authentication.UNCKerberos.NamePasswordCallbackHandler

Unclassified - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode

Constant Unclassified=1

union(Set<T>, Set<T>) - Static method in class net.sourceforge.seqware.pipeline.tools.SetOperations

UNKNOWN - Static variable in class net.sourceforge.seqware.common.module.ReturnValue

Constant UNKNOWN=130

unmarshal(String) - Method in class io.seqware.webservice.adapter.DateFormatterAdapter

unmarshal(String) - Method in class io.seqware.webservice.adapter.TimestampFormatterAdapter

unmarshal(FileList) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeFileSet

unmarshal(IUSList) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeIUSSortedSet

unmarshal(LaneList) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeLaneSortedSet

unmarshal(String) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeXML

unMarshal(T, Reader) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject

Turn an XML stream into an object, if possible.

unMarshal(Document, T) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject

Turn an XML stream into an object, if possible.

unMarshal(JaxbObject, Object, String) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools

unMarshal.

unpackageBundle(File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

unpackageBundle.

unpackageBundleFromS3(String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

unpackageBundleFromS3.

unpackArchive(File, File, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.ZipFileUtil

Unpack a zip file

UnZip - Class in net.sourceforge.seqware.pipeline.tools

UnZip class.

UnZip() - Constructor for class net.sourceforge.seqware.pipeline.tools.UnZip

unzipFile(File, File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

FIXME: should make this optional to keep the original file

unzipPkg(String) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner

FIXME: this needs to be migrated to something that is ZIP64 aware.

update(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService

update.

update(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

update.

update(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

update.

update(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService

update.

update(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService

update.

update(Integer, FileAttribute) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService

update.

update(Registration, File) - Method in interface net.sourceforge.seqware.common.business.FileService

update.

update(File) - Method in interface net.sourceforge.seqware.common.business.FileService

update.

update(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl

update.

update(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

update.

update(Registration, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

update.

update(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl

update.

update(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl

update.

update(Integer, FileAttribute) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl

update.

update(File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

update.

update(Registration, File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

update.

update(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl

update.

update(Registration, Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl

update.

update(IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

update.

update(Registration, IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

update.

update(Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

update.

update(Registration, Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

update.

update(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl

update.

update(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl

update.

update(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl

update.

update(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl

update.

update(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl

update.

update(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl

update.

update(Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

update.

update(Registration, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

update.

update(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl

update.

update(RegistrationDTO) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl

update.

update(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

update.

update(Registration, Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

update.

update(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

update.

update(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

update.

update(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl

update.

update(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl

update.

update(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl

update.

update(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl

update.

update(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl

update.

update(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl

update.

update(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl

update.

update(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

update.

update(Registration, Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

update.

update(StudyType) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl

update.

update(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl

update.

update(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl

update.

update(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl

update.

update(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl

update.

update(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl

update.

update(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl

update.

update(WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

update.

update(WorkflowRun, List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

update.

update(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

update.

update(Registration, WorkflowRun, List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

update.

update(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

update.

update(Registration, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

update.

update(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService

update.

update(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService

update.

update(IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService

update.

update(Registration, IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService

update.

update(Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService

update.

update(Registration, Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService

update.

update(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService

update.

update(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService

update.

update(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService

update.

update(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService

update.

update(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService

update.

update(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService

update.

update(Registration, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

update.

update(Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

update.

update(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService

update.

update(RegistrationDTO) - Method in interface net.sourceforge.seqware.common.business.RegistrationService

update.

update(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService

update.

update(Registration, Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService

update.

update(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

update.

update(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

update.

update(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService

update.

update(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService

update.

update(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService

update.

update(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService

update.

update(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService

update.

update(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService

update.

update(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService

update.

update(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService

update.

update(Registration, Study) - Method in interface net.sourceforge.seqware.common.business.StudyService

update.

update(StudyType) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService

update.

update(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService

update.

update(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService

update.

update(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService

update.

update(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService

update.

update(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService

update.

update(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService

update.

update(WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

update.

update(WorkflowRun, List<Integer>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

update.

update(Registration, WorkflowRun, List<Integer>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

update.

update(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

update.

update(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

update.

update(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

update.

update(ExperimentAttribute) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO

update.

update(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

update.

update(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

update.

update(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO

update.

update(ExperimentLink) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO

update.

update(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO

update.

update(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO

update.

update(FileAttribute) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO

update.

update(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

update.

update(Registration, File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

update.

update(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate

update.

update(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

update.

update(Registration, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

update.

update(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate

update.

update(ExperimentLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate

update.

update(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate

update.

update(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate

update.

update(FileAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate

update.

update(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

update.

update(Registration, File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

update.

update(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate

update.

update(Registration, Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate

update.

update(IUSAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate

update.

update(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

update.

update(Registration, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

update.

update(IUSLink) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO

update.

update(IUSLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate

update.

update(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO

update.

update(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate

update.

update(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

update.

update(Registration, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

update.

update(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO

update.

update(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate

update.

update(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate

update.

update(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

update.

update(Registration, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

update.

update(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate

update.

update(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate

update.

update(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate

update.

update(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate

update.

update(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate

update.

update(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate

update.

update(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate

update.

update(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate

update.

update(SampleAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate

update.

update(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

update.

update(Registration, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

update.

update(SampleLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate

update.

update(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

update.

update(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

update.

update(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate

update.

update(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate

update.

update(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate

update.

update(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate

update.

update(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate

update.

update(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate

update.

update(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate

update.

update(StudyAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate

update.

update(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

update.

update(Registration, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

update.

update(StudyLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate

update.

update(StudyType) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate

update.

update(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate

update.

update(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

update.

update(Registration, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

update.

update(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate

update.

update(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate

update.

update(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate

update.

update(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate

update.

update(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate

update.

update(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

update.

update(WorkflowRun, List<Integer>) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

update.

update(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

update.

update(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate

update.

update(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate

update.

update(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO

update.

update(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO

update.

update(IUSAttribute) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO

update.

update(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

update.

update(Registration, IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

update.

update(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

update.

update(Registration, Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

update.

update(ProcessingAttribute) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO

update.

update(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

update.

update(Registration, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

update.

update(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO

update.

update(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO

update.

update(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO

update.

update(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO

update.

update(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO

update.

update(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO

update.

update(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO

update.

update(Registration) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO

update.

update(SampleAttribute) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO

update.

update(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

update.

update(Registration, Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

update.

update(SampleLink) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO

update.

update(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

update.

update(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

update.

update(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO

update.

update(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO

update.

update(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO

update.

update(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO

update.

update(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO

update.

update(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO

update.

update(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO

update.

update(StudyAttribute) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO

update.

update(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

update.

update(Registration, Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

update.

update(StudyLink) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO

update.

update(StudyType) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO

update.

update(WorkflowAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO

update.

update(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

update.

update(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

update.

update(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO

update.

update(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO

update.

update(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO

update.

update(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO

update.

update(WorkflowRunAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO

update.

update(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

update.

update(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

update.

update(WorkflowRun, List<Integer>) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

update.

update(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO

update.

update(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO

update.

update_processing_event(int, ReturnValue) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

update_processing_event.

update_processing_event(int, ReturnValue) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

update_processing_event.

update_processing_event(int, ReturnValue) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

update_processing_event.

update_processing_event(int, ReturnValue) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

update_processing_event.

update_processing_status(int, ProcessingStatus) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

update_processing_status.

update_processing_status(int, ProcessingStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

update_processing_status.

update_processing_status(int, ProcessingStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

update_processing_status.

update_processing_status(int, ProcessingStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

update_processing_status.

update_processing_workflow_run(int, int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

update_processing_workflow_run.

update_processing_workflow_run(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

update_processing_workflow_run.

update_processing_workflow_run(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

update_processing_workflow_run.

update_processing_workflow_run(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

update_processing_workflow_run.

update_workflow_run(int, String, String, WorkflowRunStatus, String, String, String, String, String, String, String, String, Set<Integer>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

update_workflow_run.

update_workflow_run(int, String, String, WorkflowRunStatus, String, String, String, String, String, String, String, String, Set<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

update_workflow_run.

update_workflow_run(int, String, String, WorkflowRunStatus, String, String, String, String, String, String, String, String, Set<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

update_workflow_run.

update_workflow_run(int, String, String, WorkflowRunStatus, String, String, String, String, String, String, String, String, Set<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

update_workflow_run.

updateAttribute(AttributeDto) - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource

updateAttribute.

updateAttribute(AttributeDto) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource

updateAttribute.

updateDetached(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService

updateDetached.

updateDetached(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

updateDetached.

updateDetached(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService

updateDetached.

updateDetached(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService

updateDetached.

updateDetached(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService

updateDetached.

updateDetached(File) - Method in interface net.sourceforge.seqware.common.business.FileService

updateDetached.

updateDetached(Registration, File) - Method in interface net.sourceforge.seqware.common.business.FileService

updateDetached.

updateDetached(FileType) - Method in interface net.sourceforge.seqware.common.business.FileTypeService

updateDetached.

updateDetached(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl

updateDetached.

updateDetached(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

updateDetached.

updateDetached(Registration, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl

updateDetached.

updateDetached(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl

updateDetached.

updateDetached(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl

updateDetached.

updateDetached(File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

updateDetached.

updateDetached(Registration, File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl

updateDetached.

updateDetached(FileType) - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl

updateDetached.

updateDetached(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl

updateDetached.

updateDetached(Registration, Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl

updateDetached.

updateDetached(IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

updateDetached.

updateDetached(Registration, IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl

updateDetached.

updateDetached(Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

updateDetached.

updateDetached(Registration, Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

updateDetached.

updateDetached(LibrarySelection) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl

updateDetached.

updateDetached(LibrarySource) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl

updateDetached.

updateDetached(LibraryStrategy) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl

updateDetached.

updateDetached(Organism) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl

updateDetached.

updateDetached(Platform) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl

updateDetached.

updateDetached(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl

updateDetached.

updateDetached(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl

updateDetached.

updateDetached(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl

updateDetached.

updateDetached(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl

updateDetached.

updateDetached(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl

updateDetached.

updateDetached(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl

updateDetached.

updateDetached(Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

updateDetached.

updateDetached(Registration, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl

updateDetached.

updateDetached(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl

updateDetached.

updateDetached(Registration) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl

updateDetached.

updateDetached(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

updateDetached.

updateDetached(Registration, Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl

updateDetached.

updateDetached(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

updateDetached.

updateDetached(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl

updateDetached.

updateDetached(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl

updateDetached.

updateDetached(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl

updateDetached.

updateDetached(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl

updateDetached.

updateDetached(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl

updateDetached.

updateDetached(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl

updateDetached.

updateDetached(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl

updateDetached.

updateDetached(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl

updateDetached.

updateDetached(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

updateDetached.

updateDetached(Registration, Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

updateDetached.

updateDetached(StudyType) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl

updateDetached.

updateDetached(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl

updateDetached.

updateDetached(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl

updateDetached.

updateDetached(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl

updateDetached.

updateDetached(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl

updateDetached.

updateDetached(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl

updateDetached.

updateDetached(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl

updateDetached.

updateDetached(WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

updateDetached.

updateDetached(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

updateDetached.

updateDetached(Registration, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

updateDetached.

updateDetached(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService

updateDetached.

updateDetached(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService

updateDetached.

updateDetached(IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService

updateDetached.

updateDetached(Registration, IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService

updateDetached.

updateDetached(Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService

updateDetached.

updateDetached(Registration, Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService

updateDetached.

updateDetached(LibrarySelection) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService

updateDetached.

updateDetached(LibrarySource) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService

updateDetached.

updateDetached(LibraryStrategy) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService

updateDetached.

updateDetached(Organism) - Method in interface net.sourceforge.seqware.common.business.OrganismService

updateDetached.

updateDetached(Platform) - Method in interface net.sourceforge.seqware.common.business.PlatformService

updateDetached.

updateDetached(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService

updateDetached.

updateDetached(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService

updateDetached.

updateDetached(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService

updateDetached.

updateDetached(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService

updateDetached.

updateDetached(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService

updateDetached.

updateDetached(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService

updateDetached.

updateDetached(Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

updateDetached.

updateDetached(Registration, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService

updateDetached.

updateDetached(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService

updateDetached.

updateDetached(Registration) - Method in interface net.sourceforge.seqware.common.business.RegistrationService

updateDetached.

updateDetached(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService

updateDetached.

updateDetached(Registration, Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService

updateDetached.

updateDetached(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

updateDetached.

updateDetached(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService

updateDetached.

updateDetached(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService

updateDetached.

updateDetached(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService

updateDetached.

updateDetached(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService

updateDetached.

updateDetached(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService

updateDetached.

updateDetached(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService

updateDetached.

updateDetached(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService

updateDetached.

updateDetached(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService

updateDetached.

updateDetached(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService

updateDetached.

updateDetached(Registration, Study) - Method in interface net.sourceforge.seqware.common.business.StudyService

updateDetached.

updateDetached(StudyType) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService

updateDetached.

updateDetached(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService

updateDetached.

updateDetached(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService

updateDetached.

updateDetached(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService

updateDetached.

updateDetached(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService

updateDetached.

updateDetached(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService

updateDetached.

updateDetached(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService

updateDetached.

updateDetached(WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService

updateDetached.

updateDetached(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

updateDetached.

updateDetached(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService

updateDetached.

updateDetached(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

updateDetached.

updateDetached(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO

updateDetached.

updateDetached(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO

updateDetached.

updateDetached(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO

updateDetached.

updateDetached(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO

updateDetached.

updateDetached(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

updateDetached.

updateDetached(Registration, File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO

updateDetached.

updateDetached(FileType) - Method in interface net.sourceforge.seqware.common.dao.FileTypeDAO

updateDetached.

updateDetached(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

updateDetached.

updateDetached(Registration, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

updateDetached.

updateDetached(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate

updateDetached.

updateDetached(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate

updateDetached.

updateDetached(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate

updateDetached.

updateDetached(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

updateDetached.

updateDetached(Registration, File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate

updateDetached.

updateDetached(FileType) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate

updateDetached.

updateDetached(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate

updateDetached.

updateDetached(Registration, Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate

updateDetached.

updateDetached(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

updateDetached.

updateDetached(Registration, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate

updateDetached.

updateDetached(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

updateDetached.

updateDetached(Registration, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate

updateDetached.

updateDetached(LibrarySelection) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate

updateDetached.

updateDetached(LibrarySource) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate

updateDetached.

updateDetached(LibraryStrategy) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate

updateDetached.

updateDetached(Organism) - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate

updateDetached.

updateDetached(Platform) - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate

updateDetached.

updateDetached(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

updateDetached.

updateDetached(Registration, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate

updateDetached.

updateDetached(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate

updateDetached.

updateDetached(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate

updateDetached.

updateDetached(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate

updateDetached.

updateDetached(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate

updateDetached.

updateDetached(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate

updateDetached.

updateDetached(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate

updateDetached.

updateDetached(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate

updateDetached.

updateDetached(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate

updateDetached.

updateDetached(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

updateDetached.

updateDetached(Registration, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate

updateDetached.

updateDetached(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

updateDetached.

updateDetached(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate

updateDetached.

updateDetached(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate

updateDetached.

updateDetached(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate

updateDetached.

updateDetached(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate

updateDetached.

updateDetached(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate

updateDetached.

updateDetached(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate

updateDetached.

updateDetached(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate

updateDetached.

updateDetached(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate

updateDetached.

updateDetached(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

updateDetached.

updateDetached(Registration, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

updateDetached.

updateDetached(StudyType) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate

updateDetached.

updateDetached(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

updateDetached.

updateDetached(Registration, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

updateDetached.

updateDetached(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate

updateDetached.

updateDetached(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate

updateDetached.

updateDetached(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate

updateDetached.

updateDetached(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate

updateDetached.

updateDetached(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

updateDetached.

updateDetached(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

updateDetached.

updateDetached(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate

updateDetached.

updateDetached(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate

updateDetached.

updateDetached(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO

updateDetached.

updateDetached(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO

updateDetached.

updateDetached(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

updateDetached.

updateDetached(Registration, IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO

updateDetached.

updateDetached(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

updateDetached.

updateDetached(Registration, Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO

updateDetached.

updateDetached(LibrarySelection) - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO

updateDetached.

updateDetached(LibrarySource) - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO

updateDetached.

updateDetached(LibraryStrategy) - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO

updateDetached.

updateDetached(Organism) - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO

updateDetached.

updateDetached(Platform) - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO

updateDetached.

updateDetached(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

updateDetached.

updateDetached(Registration, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO

updateDetached.

updateDetached(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO

updateDetached.

updateDetached(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO

updateDetached.

updateDetached(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO

updateDetached.

updateDetached(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO

updateDetached.

updateDetached(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO

updateDetached.

updateDetached(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO

updateDetached.

updateDetached(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO

updateDetached.

updateDetached(Registration) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO

updateDetached.

updateDetached(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

updateDetached.

updateDetached(Registration, Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO

updateDetached.

updateDetached(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

updateDetached.

updateDetached(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO

updateDetached.

updateDetached(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO

updateDetached.

updateDetached(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO

updateDetached.

updateDetached(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO

updateDetached.

updateDetached(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO

updateDetached.

updateDetached(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO

updateDetached.

updateDetached(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO

updateDetached.

updateDetached(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO

updateDetached.

updateDetached(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

updateDetached.

updateDetached(Registration, Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

updateDetached.

updateDetached(StudyType) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO

updateDetached.

updateDetached(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

updateDetached.

updateDetached(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO

updateDetached.

updateDetached(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO

updateDetached.

updateDetached(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO

updateDetached.

updateDetached(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO

updateDetached.

updateDetached(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO

updateDetached.

updateDetached(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

updateDetached.

updateDetached(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO

updateDetached.

updateDetached(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO

updateDetached.

updateDetached(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO

updateDetached.

updateLane(Sample, MultipartFile, MultipartFile, String, String, Registration) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl

updateLane.

updateOwners(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl

updateOwners.

updateOwners(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService

updateOwners.

updateOwners(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate

updateOwners.

updateOwners(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO

updateOwners.

updateQuery(String) - Method in class io.seqware.pipeline.plugins.sanity.QueryRunner

updateSelectedIds(HttpServletRequest, String, boolean, List<String>) - Static method in class net.sourceforge.solexatools.util.BulkUtil

updateSelectedIds.

updateWorkflow(int, String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

updateWorkflow.

updateWorkflow(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

updateWorkflow.

updateWorkflow(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

updateWorkflow.

updateWorkflow(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

updateWorkflow.

updateWorkflowRun(WorkflowRun) - Method in interface net.sourceforge.seqware.common.metadata.Metadata

updateWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB

updateWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection

updateWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS

updateWorkflowRun(int, String, String, String, String, String, WorkflowRunStatus) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB

updateWorkflowRun.

updateWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource

updateWorkflowRun.

uploadFile(Study, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService

uploadFile.

uploadFile(Experiment, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService

uploadFile.

uploadFile(Sample, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService

uploadFile.

uploadFile(Lane, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService

uploadFile.

uploadFile(IUS, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService

uploadFile.

uploadFile(Processing, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService

uploadFile.

uploadFile(SequencerRun, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService

uploadFile.

uploadFile(Study, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

uploadFile.

uploadFile(Experiment, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

uploadFile.

uploadFile(Sample, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

uploadFile.

uploadFile(Lane, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

uploadFile.

uploadFile(IUS, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

uploadFile.

uploadFile(Processing, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

uploadFile.

uploadFile(SequencerRun, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl

uploadFile.

UploadFile - Class in net.sourceforge.seqware.common.business

UploadFile class.

UploadFile() - Constructor for class net.sourceforge.seqware.common.business.UploadFile

Constructor for UploadFile.

UploadFileController - Class in net.sourceforge.solexatools.webapp.controller

UploadFileController class.

UploadFileController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadFileController

Constructor for UploadFileController.

UploadFileController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadFileController

Constructor for UploadFileController.

UploadFileSetupController - Class in net.sourceforge.solexatools.webapp.controller

UploadFileSetupController class.

UploadFileSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController

Constructor for UploadFileSetupController.

UploadFileValidator - Class in net.sourceforge.solexatools.validation

UploadFileValidator class.

UploadFileValidator() - Constructor for class net.sourceforge.solexatools.validation.UploadFileValidator

Constructor for UploadFileValidator.

UploadSequence - Class in net.sourceforge.seqware.common.model

UploadSequence() - Constructor for class net.sourceforge.seqware.common.model.UploadSequence

Constructor for UploadSequence.

UploadSequenceController - Class in net.sourceforge.solexatools.webapp.controller

UploadSequenceController class.

UploadSequenceController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Constructor for UploadSequenceController.

UploadSequenceController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadSequenceController

Constructor for UploadSequenceController.

UploadSequenceSetupController - Class in net.sourceforge.solexatools.webapp.controller

UploadSequenceSetupController class.

UploadSequenceSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController

Constructor for UploadSequenceSetupController.

UploadSequenceValidator - Class in net.sourceforge.solexatools.validation

UploadSequenceValidator class.

UploadSequenceValidator() - Constructor for class net.sourceforge.solexatools.validation.UploadSequenceValidator

Constructor for UploadSequenceValidator.

URIOOZIEWORKFLOW - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp

url - Variable in class net.sourceforge.seqware.common.module.ReturnValue

urlLabel - Variable in class net.sourceforge.seqware.common.module.ReturnValue

useS3ServerSideEncryption - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles

useSge - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

UtilityREST - Class in io.seqware.webservice.controller

UtilityREST() - Constructor for class io.seqware.webservice.controller.UtilityREST

V

Validate - Class in net.sourceforge.seqware.common.util.filetools.validate

Validate class.

Validate() - Constructor for class net.sourceforge.seqware.common.util.filetools.validate.Validate

validate() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileLinkReportResource

validate.

validate() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileReverseHierarchyDisplayResource

validate.

validate(String) - Method in class net.sourceforge.solexatools.util.HTMLTagValidator

validate.

validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator

Validates the specified Object.

validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.FileValidator

Validates the specified Object.

validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.LaneValidator

Validates the specified Object.

validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.LoginValidator

Validates the specified Object.

validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.RegistrationValidator

Validates the specified Object.

validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator

Validates the specified Object.

validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator

Validates the specified Object.

validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunWizardValidator

Validates the specified Object.

validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.StudyValidator

Validates the specified Object.

validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator

Validates the specified Object.

validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator

Validates the specified Object.

validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.WorkflowParamValidator

Validates the specified Object.

validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.WorkflowValidator

Validates the specified Object.

validateBundle(File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle

validateBundle.

validateEmail(String, String, Errors) - Method in class net.sourceforge.solexatools.validation.LoginValidator

Validates an email address.

validateEmailAddressesMatch(String, String, Errors) - Static method in class net.sourceforge.solexatools.validation.RegistrationValidator

Determines if the registration's email address and confirm email address match.

validateEmailNotInUse(String, Errors) - Method in class net.sourceforge.solexatools.validation.RegistrationValidator

validateEmailNotInUse.

validateExists(MultipartFile, String, Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator

validateExists.

validateExpectedNumberReads(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator

validateExpectedNumberReads.

validateExpectedNumberReads(Sample, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator

validateExpectedNumberReads.

validateExpectedNumberRuns(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator

validateExpectedNumberRuns.

validateExpectedNumberRuns(Sample, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator

validateExpectedNumberRuns.

validateExtension(String, String, Integer, Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator

validateExtension.

validateExtension(MultipartFile, MultipartFile, Integer, Errors) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator

validateInvitationCode(String, Errors) - Method in class net.sourceforge.solexatools.validation.RegistrationValidator

validateInvitationCode.

validateLaneCount(SequencerRunWizardDTO, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunWizardValidator

validateLaneCount.

validateName(String, Errors) - Method in class net.sourceforge.solexatools.validation.LaneValidator

Determines if the Lane's email address and confirm email address match.

validateName(String, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator

Determines if the experiment's email address and confirm email address match.

validatePasswordsMatch(String, String, Errors) - Static method in class net.sourceforge.solexatools.validation.RegistrationValidator

Determines if the registration's password and confirm password match.

validateProtocol(String, String[], Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator

validateProtocol.

validateRefLane(SequencerRun, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator

validateRefLane.

validateTitle(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentUpdateValidator

validateTitle(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator

Determines if the experiment's email address and confirm email address match.

validateTitle(String, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator

Determines if the sample's email address and confirm email address match.

validateTitle(Study, Errors) - Method in class net.sourceforge.solexatools.validation.StudyUpdateValidator

validateTitle(Study, Errors) - Method in class net.sourceforge.solexatools.validation.StudyValidator

Determines if the experiment's email address and confirm email address match.

ValidationReportService - Interface in net.sourceforge.seqware.common.business

A collection of reports useful when verifying that data in the SeqWare meta db is correct.

ValidationReportServiceImpl - Class in net.sourceforge.seqware.common.business.impl

ValidationReportServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl

ValidationReportServiceImpl.ReportEntry - Class in net.sourceforge.seqware.common.business.impl

ValidationReportServiceImpl.ReportEntry() - Constructor for class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry

valueOf(String) - Static method in enum net.sourceforge.seqware.common.business.SampleReportService.Status

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.common.model.FileProvenanceParam

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.common.model.InvoiceState

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.common.model.ProcessingStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.common.model.SequencerRunStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.common.model.WorkflowRunStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.common.util.maptools.ReservedIniKeys

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.deciders.BasicDecider.FILE_STATUS

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.deciders.BasicDecider.PREVIOUS_RUN_STATUS

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.module.ModuleMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser.Field

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDBPluginInterface.Level

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility.HumanProvenanceFilters

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.workflow.BasicWorkflow.Job

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Module

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Requirement.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource.SEARCH_TYPE

Returns the enum constant of this type with the specified name.

values() - Static method in enum net.sourceforge.seqware.common.business.SampleReportService.Status

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.common.model.FileProvenanceParam

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.common.model.InvoiceState

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.common.model.ProcessingStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.common.model.SequencerRunStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.common.model.WorkflowRunStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.common.util.maptools.ReservedIniKeys

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.pipeline.deciders.BasicDecider.FILE_STATUS

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.pipeline.deciders.BasicDecider.PREVIOUS_RUN_STATUS

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.pipeline.module.ModuleMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser.Field

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDBPluginInterface.Level

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility.HumanProvenanceFilters

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.pipeline.workflow.BasicWorkflow.Job

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Module

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Requirement.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource.SEARCH_TYPE

Returns an array containing the constants of this enum type, in the order they are declared.

VAR_BUNDLE_DIR - Static variable in class net.sourceforge.seqware.common.util.maptools.MapTools

VAR_DATE - Static variable in class net.sourceforge.seqware.common.util.maptools.MapTools

VAR_DATETIME - Static variable in class net.sourceforge.seqware.common.util.maptools.MapTools

VAR_RANDOM - Static variable in class net.sourceforge.seqware.common.util.maptools.MapTools

VAR_TIMESTAMP - Static variable in class net.sourceforge.seqware.common.util.maptools.MapTools

VAR_UUID - Static variable in class net.sourceforge.seqware.common.util.maptools.MapTools

VERBOSE - Static variable in class io.seqware.cli.Main

verify(String, char[]) - Method in class net.sourceforge.seqware.queryengine.webservice.security.SeqWareVerifier

verifyFile(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

verifyFile.

version - Variable in class net.sourceforge.seqware.common.module.ReturnValue

VERSION - Static variable in class net.sourceforge.seqware.pipeline.module.Module

Constant VERSION="0.7.0"

VersionResource - Class in net.sourceforge.seqware.queryengine.webservice.view

VersionResource class.

VersionResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.VersionResource

W

WAIT - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

waitAndGetReturn(Process) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools

waitAndGetReturn(Process, int, int) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools

Wait on a process to finish, then parse information into return value

warn(Object) - Static method in class net.sourceforge.seqware.common.util.Log

See Category.warn(Object).

warn(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log

See Category.warn(Object,Throwable).

watchWorkflow(String, String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools

This method allows you to monitor a running Pegasus workflow using a statusCmd (typically something like "pegasus-status -l dir" and, if something goes wrong, it will return false.

watchWorkflow(String, String, int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools

This method allows you to monitor a running Pegasus workflow using a statusCmd (typically something like "pegasus-status -l dir" and, if something goes wrong, it will return a ReturnValue with exit status of ReturnValue.FAILURE, ReturnValue.PROCESSING if still running, and ReturnValue.SUCCESS if finished OK.

WF_XMLNS - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

Namespace of the Oozie workflow xml nodes.

wfCount(Sample) - Static method in class net.sourceforge.solexatools.util.TagUtils

Returns count of the Sample related Workflow Runs.

wfrAccession - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

wfrAccession - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

wfrAncesstor - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

wfrAncesstor - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob

whoAmI() - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

This tool uses the 'whoami' command to find the current user versus the user.name method.

WORKFLOW - Static variable in class io.seqware.pipeline.plugins.sanity.ProvidedBundleUserPhase5

Workflow - Class in io.seqware.webservice.generated.model

Workflow() - Constructor for class io.seqware.webservice.generated.model.Workflow

Workflow(Integer) - Constructor for class io.seqware.webservice.generated.model.Workflow

Workflow(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.Workflow

Workflow - Class in net.sourceforge.seqware.common.model

Workflow class.

Workflow() - Constructor for class net.sourceforge.seqware.common.model.Workflow

Constructor for Workflow.

Workflow - Class in net.sourceforge.seqware.pipeline.workflow

FIXME: This Workflow object should have much of the implementation move to the common package, see WorkflowTools

Workflow(Metadata, Map<String, String>) - Constructor for class net.sourceforge.seqware.pipeline.workflow.Workflow

Constructor for Workflow.

Workflow - Class in net.sourceforge.seqware.pipeline.workflowV2.model

Workflow() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow

WORKFLOW_CLASS - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility

WORKFLOW_ENGINE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility

WORKFLOW_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant WORKFLOW_NAME="Header.WORKFLOW_NAME.getTitle()"

WORKFLOW_RUN_ACCESSION - Static variable in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker

WORKFLOW_RUN_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant WORKFLOW_RUN_NAME="Header.WORKFLOW_RUN_NAME.getTitle()"

WORKFLOW_RUN_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant

Constant WORKFLOW_RUN_PREFIX="wfr_"

WORKFLOW_RUN_STATUS - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant WORKFLOW_RUN_STATUS="Header.WORKFLOW_RUN_STATUS.getTitle()"

WORKFLOW_RUN_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant WORKFLOW_RUN_SWA="Header.WORKFLOW_RUN_SWA.getTitle()"

WORKFLOW_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant WORKFLOW_SWA="Header.WORKFLOW_SWA.getTitle()"

WORKFLOW_TYPE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility

WORKFLOW_VERSION - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles

Constant WORKFLOW_VERSION="Header.WORKFLOW_VERSION.getTitle()"

WorkflowApp - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object

This class is responsible for the conversion of our AbstractWorkflowDataModel to an oozie xml workflow

WorkflowApp(AbstractWorkflowDataModel, String, Path, boolean, File, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp

WorkflowApp.BucketGenerator - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object

Encapsulates logic for the generation and iteration of buckets

WorkflowApp.BucketGenerator(boolean, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp.BucketGenerator

WorkflowAttribute - Class in io.seqware.webservice.generated.model

WorkflowAttribute() - Constructor for class io.seqware.webservice.generated.model.WorkflowAttribute

WorkflowAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.WorkflowAttribute

WorkflowAttribute(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.WorkflowAttribute

WorkflowAttribute - Class in net.sourceforge.seqware.common.model

WorkflowAttribute() - Constructor for class net.sourceforge.seqware.common.model.WorkflowAttribute

WorkflowAttributeDAO - Interface in net.sourceforge.seqware.common.dao

WorkflowAttributeDAO interface.

WorkflowAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

WorkflowAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate

WorkflowAttributeFacadeREST - Class in io.seqware.webservice.generated.controller

WorkflowAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.WorkflowAttributeFacadeREST

WorkflowClassFinder - Class in net.sourceforge.seqware.pipeline.workflowV2

WorkflowClassFinder class.

WorkflowClassFinder() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.WorkflowClassFinder

Constructor for WorkflowClassFinder.

WorkflowController - Class in net.sourceforge.solexatools.webapp.controller

WorkflowController class.

WorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowController

Constructor for WorkflowController.

WorkflowController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowController

Constructor for WorkflowController.

WorkflowDAO - Interface in net.sourceforge.seqware.common.dao

WorkflowDAO interface.

WorkflowDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

WorkflowDAOHibernate class.

WorkflowDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate

Constructor for WorkflowDAOHibernate.

WorkflowDataModelFactory - Class in net.sourceforge.seqware.pipeline.workflowV2

a utils class for creating the AbstractWorkflowDataModel, by reading the metadata.xml file, will load a Java based objectModel or XML based ObjectModel

WorkflowDataModelFactory(OptionSet, Map<String, String>, String[], Metadata) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.WorkflowDataModelFactory

WorkflowEngine - Interface in net.sourceforge.seqware.pipeline.workflowV2

WorkflowEngine interface.

WorkflowExecutable - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object

WorkflowExecutable() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable

WorkflowExecutableUtils - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus

a util class to generate Java, Perl, and DirManager for dax

WorkflowExecutableUtils() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils

WorkflowFacadeREST - Class in io.seqware.webservice.generated.controller

WorkflowFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.WorkflowFacadeREST

WorkflowIDResource - Class in net.sourceforge.seqware.webservice.resources.tables

WorkflowIDResource class.

WorkflowIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource

Constructor for WorkflowIDResource.

WorkflowInfo - Class in net.sourceforge.seqware.common.util.workflowtools

WorkflowInfo class.

WorkflowInfo() - Constructor for class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo

WorkflowLauncher - Class in net.sourceforge.seqware.pipeline.plugins

WorkflowLauncher() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher

WorkflowList - Class in net.sourceforge.seqware.common.model.lists

WorkflowList class.

WorkflowList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowList

Constructor for WorkflowList.

WorkflowListSetupController - Class in net.sourceforge.solexatools.webapp.controller

RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp

WorkflowListSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController

Constructor for WorkflowListSetupController.

WorkflowManager - Class in net.sourceforge.seqware.common.util.workflowtools

WorkflowManager class.

WorkflowManager() - Constructor for class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager

WorkflowParam - Class in io.seqware.webservice.generated.model

WorkflowParam() - Constructor for class io.seqware.webservice.generated.model.WorkflowParam

WorkflowParam(Integer) - Constructor for class io.seqware.webservice.generated.model.WorkflowParam

WorkflowParam(Integer, String, String, String) - Constructor for class io.seqware.webservice.generated.model.WorkflowParam

WorkflowParam - Class in net.sourceforge.seqware.common.model

WorkflowParam class.

WorkflowParam() - Constructor for class net.sourceforge.seqware.common.model.WorkflowParam

Constructor for WorkflowParam.

WorkflowParamController - Class in net.sourceforge.solexatools.webapp.controller

WorkflowParamController class.

WorkflowParamController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamController

Constructor for WorkflowParamController.

WorkflowParamController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamController

Constructor for WorkflowParamController.

WorkflowParamDAO - Interface in net.sourceforge.seqware.common.dao

WorkflowParamDAO interface.

WorkflowParamDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

WorkflowParamDAOHibernate class.

WorkflowParamDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate

Constructor for WorkflowParamDAOHibernate.

WorkflowParamFacadeREST - Class in io.seqware.webservice.generated.controller

WorkflowParamFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.WorkflowParamFacadeREST

WorkflowParamIDResource - Class in net.sourceforge.seqware.webservice.resources.tables

WorkflowParamIDResource class.

WorkflowParamIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamIDResource

Constructor for WorkflowParamIDResource.

WorkflowParamList - Class in net.sourceforge.seqware.common.model.lists

WorkflowParamList class.

WorkflowParamList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowParamList

Constructor for WorkflowParamList.

WorkflowParamListController - Class in net.sourceforge.solexatools.webapp.controller

WorkflowParamListController class.

WorkflowParamListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController

Constructor for WorkflowParamListController.

WorkflowParamResource - Class in net.sourceforge.seqware.webservice.resources.tables

WorkflowParamResource class.

WorkflowParamResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource

Constructor for WorkflowParamResource.

WorkflowParamService - Interface in net.sourceforge.seqware.common.business

WorkflowParamService interface.

WorkflowParamServiceImpl - Class in net.sourceforge.seqware.common.business.impl

WorkflowParamServiceImpl class.

WorkflowParamServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl

Constructor for WorkflowParamServiceImpl.

WorkflowParamSetupController - Class in net.sourceforge.solexatools.webapp.controller

WorkflowParamSetupController class.

WorkflowParamSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController

Constructor for WorkflowParamSetupController.

WorkflowParamValidator - Class in net.sourceforge.solexatools.validation

WorkflowParamValidator class.

WorkflowParamValidator() - Constructor for class net.sourceforge.solexatools.validation.WorkflowParamValidator

Constructor for WorkflowParamValidator.

WorkflowParamValue - Class in io.seqware.webservice.generated.model

WorkflowParamValue() - Constructor for class io.seqware.webservice.generated.model.WorkflowParamValue

WorkflowParamValue(Integer) - Constructor for class io.seqware.webservice.generated.model.WorkflowParamValue

WorkflowParamValue(Integer, String) - Constructor for class io.seqware.webservice.generated.model.WorkflowParamValue

WorkflowParamValue - Class in net.sourceforge.seqware.common.model

WorkflowParamValue class.

WorkflowParamValue() - Constructor for class net.sourceforge.seqware.common.model.WorkflowParamValue

Constructor for WorkflowParamValue.

WorkflowParamValueController - Class in net.sourceforge.solexatools.webapp.controller

WorkflowParamValueController class.

WorkflowParamValueController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController

Constructor for WorkflowParamValueController.

WorkflowParamValueController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController

Constructor for WorkflowParamValueController.

WorkflowParamValueDAO - Interface in net.sourceforge.seqware.common.dao

WorkflowParamValueDAO interface.

WorkflowParamValueDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

WorkflowParamValueDAOHibernate class.

WorkflowParamValueDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate

Constructor for WorkflowParamValueDAOHibernate.

WorkflowParamValueFacadeREST - Class in io.seqware.webservice.generated.controller

WorkflowParamValueFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.WorkflowParamValueFacadeREST

WorkflowParamValueIDResource - Class in net.sourceforge.seqware.webservice.resources.tables

WorkflowParamValueIDResource class.

WorkflowParamValueIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueIDResource

Constructor for WorkflowParamValueIDResource.

WorkflowParamValueList - Class in net.sourceforge.seqware.common.model.lists

WorkflowParamValueList class.

WorkflowParamValueList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList

Constructor for WorkflowParamValueList.

WorkflowParamValueResource - Class in net.sourceforge.seqware.webservice.resources.tables

WorkflowParamValueResource class.

WorkflowParamValueResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource

Constructor for WorkflowParamValueResource.

WorkflowParamValueService - Interface in net.sourceforge.seqware.common.business

WorkflowParamValueService interface.

WorkflowParamValueServiceImpl - Class in net.sourceforge.seqware.common.business.impl

WorkflowParamValueServiceImpl class.

WorkflowParamValueServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl

Constructor for WorkflowParamValueServiceImpl.

WorkflowParamValueSetupController - Class in net.sourceforge.solexatools.webapp.controller

WorkflowParamValueSetupController class.

WorkflowParamValueSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController

Constructor for WorkflowParamValueSetupController.

WorkflowPlugin - Class in net.sourceforge.seqware.pipeline.plugin

TODO: validate at all the option below (especially link-parent-to-workflow-run) actually work!

WorkflowPlugin() - Constructor for class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin

WorkflowReport - Class in net.sourceforge.seqware.common.hibernate

WorkflowReport class.

WorkflowReport() - Constructor for class net.sourceforge.seqware.common.hibernate.WorkflowReport

WorkflowReportResource - Class in net.sourceforge.seqware.webservice.resources.queries

WorkflowReportResource class.

WorkflowReportResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowReportResource

Constructor for WorkflowReportResource.

WorkflowResource - Class in net.sourceforge.seqware.queryengine.webservice.view

WorkflowResource class.

WorkflowResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.WorkflowResource

WorkflowResource - Class in net.sourceforge.seqware.webservice.resources.tables

WorkflowResource class.

WorkflowResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowResource

Constructor for WorkflowResource.

WorkflowRun - Class in io.seqware.webservice.generated.model

WorkflowRun() - Constructor for class io.seqware.webservice.generated.model.WorkflowRun

WorkflowRun(Integer) - Constructor for class io.seqware.webservice.generated.model.WorkflowRun

WorkflowRun(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.WorkflowRun

WorkflowRun - Class in net.sourceforge.seqware.common.model

WorkflowRun class.

WorkflowRun() - Constructor for class net.sourceforge.seqware.common.model.WorkflowRun

Constructor for WorkflowRun.

WorkflowRunAttribute - Class in io.seqware.webservice.generated.model

WorkflowRunAttribute() - Constructor for class io.seqware.webservice.generated.model.WorkflowRunAttribute

WorkflowRunAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.WorkflowRunAttribute

WorkflowRunAttribute(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.WorkflowRunAttribute

WorkflowRunAttribute - Class in net.sourceforge.seqware.common.model

WorkflowRunAttribute() - Constructor for class net.sourceforge.seqware.common.model.WorkflowRunAttribute

WorkflowRunAttributeDAO - Interface in net.sourceforge.seqware.common.dao

WorkflowRunAttributeDAO interface.

WorkflowRunAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

WorkflowRunAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate

WorkflowRunAttributeFacadeREST - Class in io.seqware.webservice.generated.controller

WorkflowRunAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.WorkflowRunAttributeFacadeREST

WorkflowRunController - Class in net.sourceforge.solexatools.webapp.controller

WorkflowRunController class.

WorkflowRunController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowRunController

Constructor for WorkflowRunController.

WorkflowRunController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowRunController

Constructor for WorkflowRunController.

WorkflowRunConventionsPlugin - Class in net.sourceforge.seqware.pipeline.plugins.checkdb.plugins

Checks the metadb for orphans that are not connected to any other entities.

WorkflowRunConventionsPlugin() - Constructor for class net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.WorkflowRunConventionsPlugin

WorkflowRunDAO - Interface in net.sourceforge.seqware.common.dao

WorkflowRunDAO interface.

WorkflowRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

WorkflowRunDAOHibernate class.

WorkflowRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate

Constructor for WorkflowRunDAOHibernate.

WorkflowRunFacadeREST - Class in io.seqware.webservice.generated.controller

WorkflowRunFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.WorkflowRunFacadeREST

WorkflowRunFilesInitialPopulationPlugin - Class in net.sourceforge.seqware.pipeline.plugins

This plugin does the initial population of workflow run files in order to track input files

WorkflowRunFilesInitialPopulationPlugin() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin

Constructor for HelloWorld.

WorkflowRunHtmlUtil - Class in net.sourceforge.solexatools.util

WorkflowRunHtmlUtil class.

WorkflowRunHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil

WorkflowRunIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries

WorkflowRunIdFilesResource class.

WorkflowRunIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIdFilesResource

Constructor for WorkflowRunIdFilesResource.

WorkflowRunIDProcessingsResource - Class in net.sourceforge.seqware.webservice.resources.queries

WorkflowRunIDProcessingsResource class.

WorkflowRunIDProcessingsResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDProcessingsResource

Constructor for WorkflowRunIDProcessingsResource.

WorkflowRunIDResource - Class in net.sourceforge.seqware.webservice.resources.tables

WorkflowRunIDResource class.

WorkflowRunIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource

Constructor for WorkflowRunIDResource.

WorkflowRunIDsFilter - Class in net.sourceforge.seqware.webservice.resources.filters

We presume there is either a runId or a testId, not both.

WorkflowRunIDsFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter

WorkflowRunIDWorkflowResource - Class in net.sourceforge.seqware.webservice.resources.queries

WorkflowRunIDWorkflowResource class.

WorkflowRunIDWorkflowResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDWorkflowResource

Constructor for WorkflowRunIDWorkflowResource.

WorkflowRunList - Class in net.sourceforge.seqware.common.model.lists

WorkflowRunList class.

WorkflowRunList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowRunList

Constructor for WorkflowRunList.

WorkflowRunList2 - Class in net.sourceforge.seqware.common.model.lists

WorkflowRunList2 class.

WorkflowRunList2() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowRunList2

Constructor for WorkflowRunList2.

WorkflowRunParam - Class in io.seqware.webservice.generated.model

WorkflowRunParam() - Constructor for class io.seqware.webservice.generated.model.WorkflowRunParam

WorkflowRunParam(Integer) - Constructor for class io.seqware.webservice.generated.model.WorkflowRunParam

WorkflowRunParam - Class in net.sourceforge.seqware.common.model

WorkflowRunParam class.

WorkflowRunParam() - Constructor for class net.sourceforge.seqware.common.model.WorkflowRunParam

Constructor for WorkflowRunParam.

WorkflowRunParamDAO - Interface in net.sourceforge.seqware.common.dao

WorkflowRunParamDAO interface.

WorkflowRunParamDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate

WorkflowRunParamDAOHibernate class.

WorkflowRunParamDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate

Constructor for WorkflowRunParamDAOHibernate.

WorkflowRunParamFacadeREST - Class in io.seqware.webservice.generated.controller

WorkflowRunParamFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.WorkflowRunParamFacadeREST

WorkflowRunParamService - Interface in net.sourceforge.seqware.common.business

WorkflowRunParamService interface.

WorkflowRunParamServiceImpl - Class in net.sourceforge.seqware.common.business.impl

WorkflowRunParamServiceImpl class.

WorkflowRunParamServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl

Constructor for WorkflowRunParamServiceImpl.

WorkflowRunReport - Class in net.sourceforge.seqware.common.hibernate

Reports on workflow run metadata, returning either all workflow runs, all runs of a particular workflow, or a specific workflow run.

WorkflowRunReport() - Constructor for class net.sourceforge.seqware.common.hibernate.WorkflowRunReport

WorkflowRunReporter - Class in net.sourceforge.seqware.pipeline.plugins

WorkflowRunReporter class.

WorkflowRunReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter

Constructor for WorkflowRunReporter.

WorkflowRunReportResource - Class in net.sourceforge.seqware.webservice.resources.queries

WorkflowRunReportResource class.

WorkflowRunReportResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource

Constructor for WorkflowRunReportResource.

WorkflowRunReportRow - Class in net.sourceforge.seqware.common.hibernate.reports

Contains the workflow's Processing events, the parent Processings, the input files, the output files, the identity and library samples, as well as the total running time.

WorkflowRunReportRow() - Constructor for class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow

WorkflowRunResource - Class in net.sourceforge.seqware.webservice.resources.tables

WorkflowRunResource class.

WorkflowRunResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource

Constructor for WorkflowRunResource.

WorkflowRuns - Class in io.seqware

WorkflowRuns() - Constructor for class io.seqware.WorkflowRuns

WorkflowRunService - Interface in net.sourceforge.seqware.common.business

WorkflowRunService interface.

WorkflowRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl

WorkflowRunServiceImpl class.

WorkflowRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl

Constructor for WorkflowRunServiceImpl.

WorkflowRunSetupController - Class in net.sourceforge.solexatools.webapp.controller

WorkflowRunSetupController class.

WorkflowRunSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController

WorkflowRunsFilter - Class in net.sourceforge.seqware.webservice.resources.filters

We presume there is either a runId or a testId, not both.

WorkflowRunsFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter

WorkflowRunStatus - Enum in net.sourceforge.seqware.common.model

WorkflowRunStatusResource - Class in net.sourceforge.seqware.queryengine.webservice.view

WorkflowRunStatusResource class.

WorkflowRunStatusResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.WorkflowRunStatusResource

WorkflowRuntimeResource - Class in net.sourceforge.seqware.webservice.resources.queries

WorkflowRuntimeResource class.

WorkflowRuntimeResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRuntimeResource

Constructor for WorkflowRuntimeResource.

WorkflowService - Interface in net.sourceforge.seqware.common.business

WorkflowService interface.

workflowService - Variable in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController

WorkflowServiceImpl - Class in net.sourceforge.seqware.common.business.impl

WorkflowServiceImpl class.

WorkflowServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl

Constructor for WorkflowServiceImpl.

WorkflowSetupController - Class in net.sourceforge.solexatools.webapp.controller

WorkflowSetupController class.

WorkflowSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController

Constructor for WorkflowSetupController.

WorkflowStatusChecker - Class in net.sourceforge.seqware.pipeline.plugins

This plugin lets you monitor the status of running workflows and updates the metadata object with their status.

WorkflowStatusChecker() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker

Constructor for WorkflowStatusChecker.

WorkflowTools - Class in net.sourceforge.seqware.common.util.workflowtools

This class provides methods for dealing with Pegasus workflow log directories for example watching a directory to detect when a workflow has failed or finished.

WorkflowTools() - Constructor for class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools

workflowTools - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow

WorkflowV2Utility - Class in net.sourceforge.seqware.pipeline.workflowV2

Utility methods that have been refactored out.

WorkflowV2Utility() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility

WorkflowValidator - Class in net.sourceforge.solexatools.validation

WorkflowValidator class.

WorkflowValidator() - Constructor for class net.sourceforge.solexatools.validation.WorkflowValidator

Constructor for WorkflowValidator.

WorkflowXmlParser - Class in net.sourceforge.seqware.pipeline.workflowV2

WorkflowXmlParser() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.WorkflowXmlParser

wrapup() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel

to be Overridden by the workflow author

write(String, File) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

writer() - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter

writeScript(String, File) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

WRSTDERR - Static variable in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter

WRSTDOUT - Static variable in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter

WS_Check - Class in io.seqware.pipeline.plugins.sanity.checks

Checks that the database you're pointing to (if there is one) is consistent with the web service you're pointing to

WS_Check() - Constructor for class io.seqware.pipeline.plugins.sanity.checks.WS_Check

WS_PASS - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys

WS_URL - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys

WS_USER - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys

X

XmlizeFileSet - Class in net.sourceforge.seqware.common.model.adapters

XmlizeFileSet class.

XmlizeFileSet() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeFileSet

XmlizeIUSSortedSet - Class in net.sourceforge.seqware.common.model.adapters

XmlizeIUSSortedSet class.

XmlizeIUSSortedSet() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeIUSSortedSet

XmlizeLaneSortedSet - Class in net.sourceforge.seqware.common.model.adapters

XmlizeLaneSortedSet class.

XmlizeLaneSortedSet() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeLaneSortedSet

XmlizeXML - Class in net.sourceforge.seqware.common.model.adapters

XmlizeXML class.

XmlizeXML() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeXML

XmlTools - Class in net.sourceforge.seqware.common.util.xmltools

XmlTools class.

XmlTools() - Constructor for class net.sourceforge.seqware.common.util.xmltools.XmlTools

XmlWorkflowDataModel - Class in net.sourceforge.seqware.pipeline.workflowV2.model

XmlWorkflowDataModel() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.XmlWorkflowDataModel

XSI - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag

Z

Zip - Class in net.sourceforge.seqware.pipeline.tools

Zip class.

Zip() - Constructor for class net.sourceforge.seqware.pipeline.tools.Zip

zipDirectoryRecursive(File, File, String, boolean, boolean) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

zipDirectoryRecursive.

ZipFileUtil - Class in net.sourceforge.solexatools.util

ZipFileUtil class.

ZipFileUtil() - Constructor for class net.sourceforge.solexatools.util.ZipFileUtil

zipListFileRecursiveOld(List<File>, File, String, String, boolean) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools

zipListFileRecursiveOld.

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